Moderator: Sej Modha

gravatar for Sej Modha
Sej Modha3.8k
Reputation:
3,800
Status:
Trusted
Location:
Glasgow, UK
Twitter:
SejModha
Last seen:
4 hours ago
Joined:
4 years, 11 months ago
Email:
s*******@gmail.com

Posts by Sej Modha

<prev • 605 results • page 1 of 61 • next >
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Comment: C: genetics mutations and phenotype
... Hi There, could you please explain how this is related to bioinformatics and what is the specific bioinformatics problem being tackled? ...
written 15 days ago by Sej Modha3.8k
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Comment: C: About ptt files from gbk files
... What have you tried so far? There are a few Perl and/or Python scripts available to do this. ...
written 15 days ago by Sej Modha3.8k
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Comment: C: Tests and programs to know if any sequence is well assembled?
... If you want to assess the quality of the assembly then you can use [QUAST][1]. [1]: http://bioinf.spbau.ru/quast ...
written 23 days ago by Sej Modha3.8k
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Comment: C: VirusDetect and the depth of coverage
... You could contact the developer directly about this. ...
written 23 days ago by Sej Modha3.8k
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Comment: C: pathogenic bacteria in the SRA database
... You can limit SRA search to organism or taxonomy ID of interest, for example, https://www.ncbi.nlm.nih.gov/sra?term=%22Acinetobacter%20baumannii%22%5BOrganism%5D%20&cmd=DetailsSearch ...
written 24 days ago by Sej Modha3.8k
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Comment: C: Is there a single header file somewhere I can use to read bam?
... Sorry, I updated my comment accordingly. Is there a specific reason why you are not planning to use htslib? ...
written 25 days ago by Sej Modha3.8k
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Comment: C: Is there a single header file somewhere I can use to read bam?
... Not sure about the language you are using for your code but it is easy to use a range of Python or Java libraries in your program. If you are using Python then you could use [pysam][1] (it uses htslib) and if you are using Java then you could use [htsjdk][2]. [1]: https://pysam.readthedocs.io/en ...
written 25 days ago by Sej Modha3.8k
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Comment: C: Can Orthofinder produce FastA?
... Would the following option be relevant in your case? os Stop after writing sequence files for orthogroups (requires '-M msa') ...
written 25 days ago by Sej Modha3.8k
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Comment: C: How can I make a .bed file from my fasta?
... Do you have some sort of coordinates of these proteins in a genome? Why do you want to save this data in the [BED format][1]? [1]: https://genome.ucsc.edu/FAQ/FAQformat.html#format1 ...
written 28 days ago by Sej Modha3.8k
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Comment: C: Download STRING database with Protein name
... You can use [BioMart][1] to convert Ensembl IDs to the gene names. [1]: https://www.ensembl.org/biomart/martview/526cd728a57fd0c7642044c4e2f2ebc6 ...
written 5 weeks ago by Sej Modha3.8k

Latest awards to Sej Modha

Teacher 28 days ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Scholar 28 days ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Scholar 10 weeks ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Scholar 10 weeks ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Scholar 3 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Scholar 3 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Help with ggtree tip labeling in R
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Help with ggtree tip labeling in R
Scholar 4 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Scholar 5 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Appreciated 7 months ago, created a post with more than 5 votes. For A: NCBI Protein GI to Genome Accession
Scholar 8 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Appreciated 8 months ago, created a post with more than 5 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 9 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession

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