User: Sej Modha

gravatar for Sej Modha
Sej Modha2.8k
Reputation:
2,780
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Location:
Glasgow, UK
Website:
http://bioinformatics....
Twitter:
SejModha
Last seen:
1 day, 2 hours ago
Joined:
4 years, 4 months ago
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s*******@gmail.com

Posts by Sej Modha

<prev • 433 results • page 1 of 44 • next >
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Comment: C: The --contig option for SPAdes
... Taken from the SPAdes [manual][1]: #### Additional contigs > In case you have contigs of the same genome generated by other > assembler(s) and you wish to merge them into SPAdes assembly, you can > specify additional contigs using --trusted-contigs or > --untrusted-contigs. First optio ...
written 5 days ago by Sej Modha2.8k
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Comment: C: Judging best assembly
... I would definitely run more than one assembler preferably with multiple k-mer values and then compare the assemblies using [QUAST][1]. [1]: http://quast.sourceforge.net/ ...
written 15 days ago by Sej Modha2.8k
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Comment: C: Removing a chromosome from a fasta file
... Have you tried any tools/commands? There are multiple threads on this forum about modifying fasta files: https://www.biostars.org/p/210505/ https://www.biostars.org/p/143617/ https://www.biostars.org/p/230686/ ...
written 17 days ago by Sej Modha2.8k
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Comment: C: Converting .maf file to .mfa file
... I have never used this before but have you tried this? https://github.com/dentearl/mafTools/tree/master/mafToFastaStitcher ...
written 17 days ago by Sej Modha2.8k
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Comment: C: Retrieve reference genome for a taxonomic id from NCBI automaticaly
... Are you trying to link E. coli taxonomy ID `txid511145` to assembly ID `161521` which is a Mycobacterium tuberculosis assembly? ...
written 24 days ago by Sej Modha2.8k
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Comment: C: kraken: unable to download the databases from ncbi
... Hi there, I have updated the script to explicitly specify the dtype, updated version of the script is available to download from the [github][1]. [1]: https://raw.githubusercontent.com/sejmodha/MiscScripts/master/UpdateKrakenDatabases.py ...
written 4 weeks ago by Sej Modha2.8k
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Comment: C: how to replace <*> column with nucleotide in python or R or Shell
... Can you post something you have already tried? ...
written 4 weeks ago by Sej Modha2.8k
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Comment: C: RefSeq ID to TaxID?
... Try this: esearch -db nucleotide -query "NZ_LFWC01000004.1"|esummary|xtract -pattern TaxId -element TaxId ...
written 5 weeks ago by Sej Modha2.8k
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Comment: C: RefSeq ID to TaxID?
... I guess one has to be careful with the [db_xref][1] tag, it can often contain identifiers linking to other databases such as UniProtKB. [1]: https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/ ...
written 5 weeks ago by Sej Modha2.8k
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Answer: A: RefSeq ID to TaxID?
... Using [NCBI Unix eutilities][1]: esearch -db nucleotide -query "NZ_LFWC01000004.1"|esummary|xtract -pattern TaxId -element TaxId [1]: https://www.ncbi.nlm.nih.gov/books/NBK179288/ ...
written 5 weeks ago by Sej Modha2.8k

Latest awards to Sej Modha

Appreciated 12 days ago, created a post with more than 5 votes. For A: NCBI Protein GI to Genome Accession
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Scholar 5 weeks ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
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Scholar 5 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Scholar 5 months ago, created an answer that has been accepted. For A: CAR parameters not work
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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: NCBI Protein GI to Genome Accession
Scholar 6 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Appreciated 6 months ago, created a post with more than 5 votes. For A: NCBI Protein GI to Genome Accession
Scholar 6 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
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Teacher 8 months ago, created an answer with at least 3 up-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
Scholar 8 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file

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