Moderator: Sej Modha

gravatar for Sej Modha
Sej Modha4.5k
Reputation:
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Location:
Glasgow, UK
Twitter:
SejModha
Last seen:
1 day, 12 hours ago
Joined:
5 years, 11 months ago
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s*******@gmail.com

Posts by Sej Modha

<prev • 694 results • page 1 of 70 • next >
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Comment: C: Mauve program will not open
... It is difficult to help without any information related to the operating system, java version you're trying to run the program with and version of the mauve you're trying to use. https://www.biostars.org/p/357878/ ...
written 6 days ago by Sej Modha4.5k
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Comment: C: ORF finder v0.4.1
... Is there any specific reason why you'd like to use an older version of this tool? ...
written 9 days ago by Sej Modha4.5k
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Comment: C: Where to find .ace format description
... There is some explanation about the ACE file format on here: https://web.archive.org/web/20100609072313/http://bcr.musc.edu/manuals/CONSED.txt ...
written 17 days ago by Sej Modha4.5k
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Comment: C: Retrieving sequence from NCBI
... Can you share an example of what sorta data you have? Do you have gene names or NCBI gene ids? ...
written 28 days ago by Sej Modha4.5k
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Comment: C: Genome size estimation using Kmergenie
... You could find out by reading Kmergenie [paper][1] [1]: https://academic.oup.com/bioinformatics/article/30/1/31/235479 ...
written 5 weeks ago by Sej Modha4.5k
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Comment: C: problem with missing input file in snakemake rule
... I am not sure why you need `rule all` for in this case as you are saving the output from each `bam` file to a single file. ...
written 6 weeks ago by Sej Modha4.5k
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Comment: C: Crystal structure of lambda phage?
... Did you try searching the [PDB][1] database? [1]: https://www.rcsb.org/ ...
written 6 weeks ago by Sej Modha4.5k
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Answer: C: problem with missing input file in snakemake rule
... My guess is that the only output that can be found from rule `map_star_SE` is a `bam` file as you have specified. If you are saving a `*.out.tab` as part of that rule then you'd have to explicitly specify that in the rule `map_star_SE` output section. ...
written 6 weeks ago by Sej Modha4.5k
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Comment: C: alternative to mauve : multiple alignments of whole genomes
... You could try [Sibelia][1] or [Mugsy][2] for whole-genome alignments and comparison. [1]: https://github.com/bioinf/Sibelia [2]: http://mugsy.sourceforge.net/ ...
written 6 weeks ago by Sej Modha4.5k
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Comment: C: how to change gtf to fasta file of cufflink, gffread
... If I understand this, are you referring to FASTA file header when you mentioned > But I get only TCONS_00033653 ID ...
written 6 weeks ago by Sej Modha4.5k

Latest awards to Sej Modha

Commentator 7 days ago, created a comment with at least 3 up-votes. For C: Help with ggtree tip labeling in R
Scholar 17 days ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Scholar 6 weeks ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Scholar 3 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Scholar 7 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Popular Question 7 months ago, created a question with more than 1,000 views. For 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
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 9 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Scholar 13 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
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Scholar 14 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Scholar 15 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Scholar 15 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: Help with ggtree tip labeling in R
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: Help with ggtree tip labeling in R
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Scholar 17 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file

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