User: Sej Modha

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Sej Modha1.3k
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SejModha
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Posts by Sej Modha

<prev • 211 results • page 1 of 22 • next >
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Answer: A: Capturing whole gene sequences from WGS metagenomics sample
... If you have assemblies from two separate assemblers then you can try [GARM][1]. [1]: http://garm-meta-assem.sourceforge.net/ ...
written 4 days ago by Sej Modha1.3k
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Answer: A: about weeSam command
... weeSAM is a custom script written by [Joseph Hughes][1] that is part of the MetaViC pipeline and available to download from https://github.com/josephhughes/Sequence-manipulation/blob/master/weeSAMv1.1 [1]: https://www.biostars.org/u/166/ ...
written 5 days ago by Sej Modha1.3k
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Answer: A: Difference between read and contig based taxonomic classification
... Read based taxonomic classification is where each read generated from a sequencing method is search against a database of known sequences to find similarity. Contig are longer sequences generated by stitching overlapping reads. Contig based classification is where these longer sequences are search a ...
written 6 days ago by Sej Modha1.3k
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Comment: C: BLAST IDs into gene names? (Diamond)
... You can accept my answer as a correct answer then! ...
written 9 days ago by Sej Modha1.3k
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Answer: A: BLAST IDs into gene names? (Diamond)
... I am not sure if you are using the latest version of DIAMOND as there is following options to get the Subject title in the tabular DIAMOND output. DIAMOND version - diamond v0.8.20.82 stitle means Subject Title ...
written 9 days ago by Sej Modha1.3k
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Answer: A: meaning of XM:i:N in Bowtie output
... You can check details about these tags here: https://gist.github.com/davfre/8596159 ...
written 12 days ago by Sej Modha1.3k
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Comment: C: Problem installing mummer
... Maybe you can download the pre-built versions available here: https://sourceforge.net/projects/mummer/files/mummer/3.23/ ...
written 12 days ago by Sej Modha1.3k
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Comment: C: Update kraken databases
... Hi, I have not built a custom db with fungi but I am sure you can modify this script to do that. ...
written 16 days ago by Sej Modha1.3k
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Comment: C: Filtering blastx by taxonomy ID
... I don't think it is possible to limit BLAST database output to a specific taxonomy ID. Maybe you can look into [DIAMOND][1] instead of running BLASTX as it's much faster than BLASTX. [1]: https://github.com/bbuchfink/diamond ...
written 18 days ago by Sej Modha1.3k
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Comment: C: How to perform bidirectional BLAST?
... You can use DIGS tool that automates this process and saves output to RDBMS for this. http://giffordlabcvr.github.io/DIGS-tool/ ...
written 18 days ago by Sej Modha1.3k

Latest awards to Sej Modha

Scholar 9 days ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Appreciated 16 days ago, created a post with more than 5 votes. For A: NCBI Protein GI to Genome Accession
Teacher 26 days ago, created an answer with at least 3 up-votes. For A: Where is the source code for legacy BLAST?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Where is the source code for legacy BLAST?
Student 7 weeks ago, asked a question with at least 3 up-votes. For 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
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Where is the source code for legacy BLAST?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Where is the source code for legacy BLAST?
Guru 4 months ago, received more than 100 upvotes.
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Where i can find complete genome of any organism?
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Where i can find complete genome of any organism?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Where is the source code for legacy BLAST?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Remove duplicate protein sequences having different fasta identifiers
Scholar 6 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: Remove duplicate protein sequences having different fasta identifiers
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Scholar 7 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
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Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: NCBI Protein GI to Genome Accession
Scholar 8 months ago, created an answer that has been accepted. For A: Correct substitution model for yeast - RAxML
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Scholar 10 months ago, created an answer that has been accepted. For A: NCBI Protein GI to Genome Accession
Scholar 10 months ago, created an answer that has been accepted. For A: NCBI Protein GI to Genome Accession

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