Moderator: Sej Modha

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Sej Modha4.7k
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SejModha
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Posts by Sej Modha

<prev • 720 results • page 1 of 72 • next >
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Comment: C: Filtering 50 biggest contigs
... You could convert multiline fasta to single line using https://www.biostars.org/p/9262/ and then extract the first 100 lines using `head` which should extract the top 50 contigs for you. ...
written 1 day ago by Sej Modha4.7k
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Comment: C: Launch a snakefile involving multiple conda environment using an snakemake speci
... Thanks for clarifying that, just to check, could you try putting `nanofilt.yaml` at the same directory level as the snakemake file and modify the file path in the script? Re-run the script and see if still get the same error? I am just wondering if snakemake is able to find the env file specified in ...
written 2 days ago by Sej Modha4.7k
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Comment: C: Launch a snakefile involving multiple conda environment using an snakemake speci
... Sorry, you're right, I misunderstood the question. Can you clarify what you mean by 'On my computer, snakemake is already installed' ? Do you mean you have snakemake installed in your base env? ...
written 2 days ago by Sej Modha4.7k
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Comment: C: Launch a snakefile involving multiple conda environment using an snakemake speci
... AFAIK, you'd need to ensure that all tools included in the Snakemake pipeline are installed in the specific environment you're running the Snakemake pipeline from. You'd need to install NanoFilt and other tools either in the new conda environment. ...
written 2 days ago by Sej Modha4.7k
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Comment: C: Biopython SeqIO.parse not functioning for all entries in a seq
... Can you post your code here? There is a `"` missing in the `for seq_record in SeqIO.parse("datafile_location, "genbank"):` loop but I guess that's a typo in the post as opposed to the code? ...
written 2 days ago by Sej Modha4.7k
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Comment: C: Keep duplicate searches with grep
... What have you tried so far? Please show some efforts before posting a question on this forum. Please have a read through https://www.biostars.org/p/357878/ ...
written 24 days ago by Sej Modha4.7k
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Answer: C: Filter record of pubmed articles on Humans.
... A short answer to this is yes, it is possible to limit records to organism==human. For example: `esearch -db pubmed -query 'Homo sapiens [Orgn]'` Learn more about eutils: https://www.ncbi.nlm.nih.gov/books/NBK179288/ PS: https://www.biostars.org/p/357878/ ...
written 6 weeks ago by Sej Modha4.7k
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Answer: A: CARD ID to UNIPROT ID
... You can use UniProt's [Retrieve/ID mapping service][1]. Paste the list of identifiers separated by the space in the query box and select From `EMBL/GenBank/DDBJ CDS` To `UniProtKB` [1]: https://www.uniprot.org/uploadlists/ ...
written 6 weeks ago by Sej Modha4.7k
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Comment: C: How to check the pattern in a specific file present in which other files in a di
... Try using `grep -f` More examples on: https://www.linuxtechi.com/linux-grep-command-with-14-different-examples/ ...
written 7 weeks ago by Sej Modha4.7k
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Answer: C: How to download data stored in git lfs
... You'd have to install `git lfs` and then use `git lfs fetch` as described in the thread below. https://github.com/git-lfs/git-lfs/issues/325 ...
written 7 weeks ago by Sej Modha4.7k

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Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Scholar 8 weeks ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Great Question 3 months ago, created a question with more than 5,000 views. For NCBI Protein GI to Genome Accession
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Help with ggtree tip labeling in R
Scholar 8 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Scholar 9 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Scholar 10 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Scholar 14 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Popular Question 15 months ago, created a question with more than 1,000 views. For NCBI Protein GI to Genome Accession
Appreciated 16 months ago, created a post with more than 5 votes. For A: NCBI Protein GI to Genome Accession
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Teacher 16 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Scholar 16 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Scholar 20 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Scholar 22 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Scholar 22 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Scholar 23 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Scholar 23 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Commentator 24 months ago, created a comment with at least 3 up-votes. For C: Help with ggtree tip labeling in R

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