<h4>fishing out tp53 RNA-Seq reads</h4>
<ul>
<li>go to <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi" rel="nofollow noreferrer">NCBI Taxonomy Browser</a></li>
<li>put <code>Anas platyrhynchos</code> as a search term</li>
<li>click on <code>Anas platyrhynchos</code></li>
<li>on the right you will have a table with <code>SRA Experiments</code>, click on <code>11,679</code></li>
<li>restrict to <code>RNA</code> and <code>paired</code> on the left</li>
<li>send it to <code>Run Selector</code></li>
<li>order it by the <code>Bases</code></li>
<li>select few top runs, like <code>SRR16082819</code></li>
</ul>
<p>Now it depends what is your exact goal. You may (separate approaches):</p>
<ul>
<li>get mallard transcriptome as complete as possible, use <code>kallisto</code> just to check that a given pair of FASTQs contains bunch of reads derived from tp53</li>
<li>use <code>STAR</code> to align it to the genome with the contig containing TP53 gene</li>
<li>one can also try to fish out the reads out of FASTQ using tp53 cDNA sequence, but this will likely miss i.e. putative alternative 5- &amp; 3-prime part of the gene</li>
</ul>

CC BY-SA 4.0
2024-02-17T15:06:16.473Z
Thank you for this insightful response! For the last part, could you add more details about this step of alignment against the genome? Namely, how exactly can I confirm the contig containing the TP53 gene is present and identified using `STAR`?
user18959
CC BY-SA 4.0
2024-02-17T16:55:31.320Z
It is this contig [NW_024009712](https://www.ncbi.nlm.nih.gov/nuccore/NW_024009712) you will have to get both the genome fasta ans GTF annotation from https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_015476345.1/
darked89
CC BY-SA 4.0
2024-02-17T16:59:39.520Z
Also you may try to align the above contig to probably more complete chicken genome to get an idea about how good is the annotation of the p53 gene in mallard/is there anything missing.
darked89
CC BY-SA 4.0
2024-02-20T23:25:46.070Z
Thank you! For clarity, how did you find that contig? Also, strangely the genome fasta file seems to be corrupted in some way (but other files work, e.g. GTF annotation). Is this genome fasta file hosted anywhere else by chance?
user18959
CC BY-SA 4.0
2024-02-21T09:40:26.823Z
I did find this updated version (from 2023-12-14) of the genome [here](https://ngdc.cncb.ac.cn/gwh/ncbi_assembly/38807/show), but is there any way to confirm that the GFF/GTF file includes TP53?
user18959
CC BY-SA 4.0
2024-02-21T09:54:20.713Z
download the annotation then: ``` zcat GCF_015476345.1_ZJU1.0_genomic.gff.gz  | grep "gene=TP53;" | more```
darked89
CC BY-SA 4.0
2024-02-21T09:58:49.330Z
That works great — thank you! Going to test this all out now
user18959
CC BY-SA 4.0
2024-02-21T10:15:36.587Z
I tried converting the GFF to GTF using [this method](https://bioinformatics.stackexchange.com/a/18234/18959) but keep hitting into: `KeyError: 'id-LOC110351722'` (perhaps due to "gene_id" key not being present for key-value pairings of the .gtf file) — trying to resolve it, but if you have any thoughts, certainly glad to receive it
user18959
CC BY-SA 4.0
2024-02-21T10:32:20.600Z
re conversion gff to gtf: this is a separate question. BTW, why you need it?
darked89
CC BY-SA 4.0
2024-02-21T10:42:13.930Z
It's part of the nf-core pipeline — it expects annotations in GTF format, but the above link only provides GFF files. I tried using [gff3_ID_generator.py](https://gff3toolkit.readthedocs.io/en/latest/FAQ.html) to generate IDs if the gff file does not have them for every feature, but the error persists
user18959
CC BY-SA 4.0
2024-02-21T11:01:43.597Z
I think I've found the solution [here](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/015/476/345/GCF_015476345.1_ZJU1.0/) where the larger repo of files are available
user18959
CC BY-SA 4.0
2024-02-21T11:07:46.760Z
Ok. Still, file another question about the gff to gtf conversion of that particular gff file. And it will be helpful if you up vote and accept the answer as a correct one
darked89
CC BY-SA 4.0
2024-02-22T00:38:32.917Z
Yep, just running and testing the pipeline with the updated fasta and gtf files to determine if TP53 is ultimately found with the nf-core pipeline (which I expect it should) — but these new files keep resulting in the pipeline terminating due to an error somewhere in the files which I'm trying to trace down
user18959
CC BY-SA 4.0
2024-03-04T05:55:57.267Z
Got it working now. These gtf files have a lot information that needs to be cleaned / corrected (e.g. missing gene IDs), but it appears to now run!
user18959
CC BY-SA 4.0
2024-02-16T10:45:21.553Z
2024-02-16T10:45:21.553Z
darked89
<p>I have been running <a href="https://nf-co.re/rnaseq/1.4.2/docs/output" rel="nofollow noreferrer">nf-core</a> in Python and it works great! But I have a seemingly simple question that I'm struggling to find an answer for online. After running the nf-core pipeline on my RNA sequencing data, Salmon is able to provide gene counts in a file named <code>salmon.merged.gene_counts.tsv</code>. This file has essentially all the information I am seeking with all counts associated to a unique gene_id. But, for a large number of these gene_ids where no specific gene_name is known, I would like to further find the corresponding DNA sequence (or corresponding transcript's RNA sequence) for each gene_id. Accordingly, my question is: where can I find the information to map the gene_id to the corresponding nucleotides of the gene's (or original transcript's) sequence?</p>
<p>(Apologies in advance if my question is missing information or overly simply and I'm overlooking something obvious — I am quite new to this all.)</p>

CC BY-SA 4.0
2024-02-15T12:18:05.737Z
Which species? Also:can you provide any examples of `gene_ids` you have problems with?
darked89
CC BY-SA 4.0
2024-02-15T12:33:52.073Z
Anas platyrhynchos (mallard) — I'm trying to actually do the inverse problem and check if [TP53](https://www.ncbi.nlm.nih.gov/gene/119714806/) is present as one of the `gene_ids`. Looking at [related data from https://midb.pnb.uconn.edu/](https://midb.pnb.uconn.edu/basic_search_php2.php?species_var=Anas+platyrhynchos+platyrhynchos&gene=TP53&gene_class=all), this gene seems to be missing there as well
user18959
CC BY-SA 4.0
2024-02-15T12:59:55.703Z
re TP53: if one search for p53 gene here: https://www.ensembl.org/Anas_platyrhynchos/Info/Index I do not see the TP53 itself, just the genes binding to it, or downstream targets. If the genome is incomplete/full of gaps then tp53 may be missing from annotation. I guess not just in ENSEMBL but from other genome assembly based as well.
darked89
CC BY-SA 4.0
2024-02-15T13:26:54.127Z
If you look at the orthologues of human TP53 (ENSEMBL), you can find them in chicken, Kakapo, Zebra finch plus a bunch of reptiles. While this is not an ultimate proof that TP53 does exist in your duck, I would expect that some duck RNA-Seq may contain at least fragments of TP53.
darked89
CC BY-SA 4.0
2024-02-15T23:29:14.457Z
Thank you for sharing these thoughts, @darked89. I suppose my simple question is: what is the best way to check the duck RNAseq data for any fragments of TP53? Any specific insights on methods and files to utilize would be helpful!
user18959
CC BY-SA 4.0
2024-02-16T04:05:25.837Z
Additionally, out of curiosity, how is it that the [TP53 gene is available on NCBI](https://www.ncbi.nlm.nih.gov/gene/119714806/) but unavailable in Ensembl's automated curation pipeline?
user18959
CC BY-SA 4.0
2024-02-16T08:35:52.977Z
re ENSEMBL mallard tp53: from the NCBI there is a link to [ENSEMBL rapid](https://rapid.ensembl.org/Anas_platyrhynchos_GCA_015476345.1/Gene/Summary?g=ENSAPLG00030005532;r=JACGAL010000063.1:128466-138874). Could be there are two mallard assemblies or at least two versions?
darked89
<rna-seq><gene-expression><transcriptome><star><salmon>
After running nf-core, is there a way to map a gene_id to a specific gene's DNA sequence?
# After running nf-core, is there a way to map a gene_id to a specific gene's DNA sequence?

(Asked by: username_0 on 2024-02-15)

I have been running [nf-core](https://nf-co.re/rnaseq/1.4.2/docs/output) in Python and it works great! But I have a seemingly simple question that I'm struggling to find an answer for online. After running the nf-core pipeline on my RNA sequencing data, Salmon is able to provide gene counts in a file named `salmon.merged.gene_counts.tsv`. This file has essentially all the information I am seeking with all counts associated to a unique gene\_id. But, for a large number of these gene\_ids where no specific gene\_name is known, I would like to further find the corresponding DNA sequence (or corresponding transcript's RNA sequence) for each gene\_id. Accordingly, my question is: where can I find the information to map the gene\_id to the corresponding nucleotides of the gene's (or original transcript's) sequence?

(Apologies in advance if my question is missing information or overly simply and I'm overlooking something obvious — I am quite new to this all.)

**Tags:** rna-seq, gene-expression, transcriptome, star, salmon
> **Comments:**
> **username_1**: Which species? Also:can you provide any examples of `gene_ids` you have problems with?  
> **username_0**: Anas platyrhynchos (mallard) — I'm trying to actually do the inverse problem and check if [TP53](https://www.ncbi.nlm.nih.gov/gene/119714806/) is present as one of the `gene_ids`. Looking at [related data from https://midb.pnb.uconn.edu/](https://midb.pnb.uconn.edu/basic_search_php2.php?species_var=Anas+platyrhynchos+platyrhynchos&gene=TP53&gene_class=all), this gene seems to be missing there as well  
> **username_1**: re TP53: if one search for p53 gene here: https://www.ensembl.org/Anas_platyrhynchos/Info/Index I do not see the TP53 itself, just the genes binding to it, or downstream targets. If the genome is incomplete/full of gaps then tp53 may be missing from annotation. I guess not just in ENSEMBL but from other genome assembly based as well.  
> **username_1**: If you look at the orthologues of human TP53 (ENSEMBL), you can find them in chicken, Kakapo, Zebra finch plus a bunch of reptiles. While this is not an ultimate proof that TP53 does exist in your duck, I would expect that some duck RNA-Seq may contain at least fragments of TP53.  
> **username_0**: Thank you for sharing these thoughts, @darked89. I suppose my simple question is: what is the best way to check the duck RNAseq data for any fragments of TP53? Any specific insights on methods and files to utilize would be helpful!  
> **username_0**: Additionally, out of curiosity, how is it that the [TP53 gene is available on NCBI](https://www.ncbi.nlm.nih.gov/gene/119714806/) but unavailable in Ensembl's automated curation pipeline?  
> **username_1**: re ENSEMBL mallard tp53: from the NCBI there is a link to [ENSEMBL rapid](https://rapid.ensembl.org/Anas_platyrhynchos_GCA_015476345.1/Gene/Summary?g=ENSAPLG00030005532;r=JACGAL010000063.1:128466-138874). Could be there are two mallard assemblies or at least two versions?  

---

## 1 answers

### Answer by username_1 on 2024-02-16. Score: 1 | Accepted answer

#### fishing out tp53 RNA-Seq reads

* go to [NCBI Taxonomy Browser](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi)
* put `Anas platyrhynchos` as a search term
* click on `Anas platyrhynchos`
* on the right you will have a table with `SRA Experiments`, click on `11,679`
* restrict to `RNA` and `paired` on the left
* send it to `Run Selector`
* order it by the `Bases`
* select few top runs, like `SRR16082819`

Now it depends what is your exact goal. You may (separate approaches):

* get mallard transcriptome as complete as possible, use `kallisto` just to check that a given pair of FASTQs contains bunch of reads derived from tp53
* use `STAR` to align it to the genome with the contig containing TP53 gene
* one can also try to fish out the reads out of FASTQ using tp53 cDNA sequence, but this will likely miss i.e. putative alternative 5- & 3-prime part of the gene

> **Comments:**
> **username_0**: Thank you for this insightful response! For the last part, could you add more details about this step of alignment against the genome? Namely, how exactly can I confirm the contig containing the TP53 gene is present and identified using `STAR`?  
> **username_1**: It is this contig [NW_024009712](https://www.ncbi.nlm.nih.gov/nuccore/NW_024009712) you will have to get both the genome fasta ans GTF annotation from https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_015476345.1/  
> **username_1**: Also you may try to align the above contig to probably more complete chicken genome to get an idea about how good is the annotation of the p53 gene in mallard/is there anything missing.  
> **username_0**: Thank you! For clarity, how did you find that contig? Also, strangely the genome fasta file seems to be corrupted in some way (but other files work, e.g. GTF annotation). Is this genome fasta file hosted anywhere else by chance?  
> **username_0**: I did find this updated version (from 2023-12-14) of the genome [here](https://ngdc.cncb.ac.cn/gwh/ncbi_assembly/38807/show), but is there any way to confirm that the GFF/GTF file includes TP53?  
> **username_1**: download the annotation then: ``` zcat GCF_015476345.1_ZJU1.0_genomic.gff.gz  | grep "gene=TP53;" | more```  
> **username_0**: That works great — thank you! Going to test this all out now  
> **username_0**: I tried converting the GFF to GTF using [this method](https://bioinformatics.stackexchange.com/a/18234/18959) but keep hitting into: `KeyError: 'id-LOC110351722'` (perhaps due to "gene_id" key not being present for key-value pairings of the .gtf file) — trying to resolve it, but if you have any thoughts, certainly glad to receive it  
> **username_1**: re conversion gff to gtf: this is a separate question. BTW, why you need it?  
> **username_0**: It's part of the nf-core pipeline — it expects annotations in GTF format, but the above link only provides GFF files. I tried using [gff3_ID_generator.py](https://gff3toolkit.readthedocs.io/en/latest/FAQ.html) to generate IDs if the gff file does not have them for every feature, but the error persists  
> **username_0**: I think I've found the solution [here](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/015/476/345/GCF_015476345.1_ZJU1.0/) where the larger repo of files are available  
> **username_1**: Ok. Still, file another question about the gff to gtf conversion of that particular gff file. And it will be helpful if you up vote and accept the answer as a correct one  
> **username_0**: Yep, just running and testing the pipeline with the updated fasta and gtf files to determine if TP53 is ultimately found with the nf-core pipeline (which I expect it should) — but these new files keep resulting in the pipeline terminating due to an error somewhere in the files which I'm trying to trace down  
> **username_0**: Got it working now. These gtf files have a lot information that needs to be cleaned / corrected (e.g. missing gene IDs), but it appears to now run!  

---

