User: vkkodali

gravatar for vkkodali
vkkodali690
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690
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United States
Last seen:
46 minutes ago
Joined:
2 years, 4 months ago
Email:
v*****@gmail.com

Posts by vkkodali

<prev • 73 results • page 1 of 8 • next >
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Comment: C: How to retrieve sets of protein sequences?
... If you just want to extract the IDs and not care about the order they are in then you can skip the `sort` at the end. Also, if you skip the `sort` at the end then the IDs will be returned in the same order they appear in the FASTA file. ...
written 4 hours ago by vkkodali690
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Comment: C: How to retrieve sets of protein sequences?
... I am able to download the FASTA sequences for all three of those IDs without an issue. How did you create the `uniprot_ids.txt` file? If you have created it on Windows then you may want to run `dos2unix` on that file to make sure it's not the line endings that are mucking things up. For checking w ...
written 6 hours ago by vkkodali690
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Comment: C: How to retrieve sets of protein sequences?
... > how can I know which proteins sequences are downloaded and which ones are not? You will have to use a unix tool like `grep` to check which IDs are in the fasta file and which ones are missing. > should I install epost and efetch ? If you have followed the instructions at http://bit.ly/en ...
written 6 hours ago by vkkodali690
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Comment: C: Bigwig format and operation
... I cannot comment on the specifics of ATAC-Seq but your data is actually in bedGraph format, as described [here](https://genome.ucsc.edu/goldenpath/help/bedgraph.html). The value in the 4th column is the Y-axis value for a graph where the X-axis values are the range between columns 2 and 3. ...
written 10 hours ago by vkkodali690
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Comment: C: Which tool can remove SignalP predicted signal peptides from FASTA file?
... If you run the commands shown above as-is you should end up with `uniprot.mat_pep.fasta` file. Are you having trouble running them? Here's the file: https://drive.google.com/open?id=1coo2uipv-zTK1F98xi09zfh6-Ahmmykt ...
written 12 hours ago by vkkodali690
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Comment: C: Filter the non-redundant NCBI database based on taxonomy
... You probably mean `txid2759` not `txid2579`. I have myself not used blast from command line this way but it is possible that the tax IDs int he local copy are the species level tax IDs where as 2759 includes all eukaryotes. ...
written 12 hours ago by vkkodali690
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Answer: A: How to retrieve sets of protein sequences?
... You can get it from UniProt directly using `curl` as follows: $ cat uniprot_ids.txt P00750 P00751 P00752 $ for acc in `cat uniprot_ids.txt` ; do curl -s "https://www.uniprot.org/uniprot/$acc.fasta" ; done > uniprot_seqs.fasta But if you choose to go with Entrez Direct, th ...
written 1 day ago by vkkodali690
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Answer: A: Filter the non-redundant NCBI database based on taxonomy
... If you don't mind using the `-remote` option, you can consider using the `-entrez_query` with `txid2759[Organism]`. ...
written 1 day ago by vkkodali690
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Answer: A: UniProtKB - mapping gene name to ID (*_HUMAN ) using python2
... Try changing your `url` to `https://www.uniprot.org/uniprot/` and `params` to: { 'query': 'gene_exact:mapk1 AND organism:homo_sapiens AND reviewed:yes', 'format': 'tab', 'columns': 'id,entry_name,genes' } ...
written 2 days ago by vkkodali690
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Answer: A: Which tool can remove SignalP predicted signal peptides from FASTA file?
... I followed your Uniprot link and clicked on the 'Download' button to download two files: 1. Download all 359 proteins in GFF format (`uniprot.gff` file) 2. Download all 359 proteins in FASTA format (`uniprot.fasta` file) Then, I processed the two files as follows: 1. Process `uniprot.gff` file to ...
written 3 days ago by vkkodali690

Latest awards to vkkodali

Scholar 6 hours ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 2 days ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 2 days ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 2 days ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 2 days ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 2 days ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 11 days ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 17 days ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 4 weeks ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 5 weeks ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 6 weeks ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 6 weeks ago, created an answer that has been accepted. For C: Strange esearch behavior
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 6 weeks ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 6 weeks ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 6 weeks ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 7 weeks ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 7 weeks ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?

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