User: Sej Modha

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Sej Modha1.7k
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Glasgow, UK
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http://bioinformatics....
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SejModha
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Posts by Sej Modha

<prev • 240 results • page 1 of 24 • next >
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Comment: C: tools to get the coverage
... bedtools genomecov is explained in depth here: http://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html ...
written 5 hours ago by Sej Modha1.7k
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Answer: A: Extract dna sequence of multiple genes from multiple bam files
... Please have a look a the answers from this post: [How to extract fasta sequence of a gene from BAM files generated using Miseq sequencing][1] [1]: https://www.biostars.org/p/175758/ ...
written 2 days ago by Sej Modha1.7k
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Answer: A: motif and domain finder
... Have you tried [InterProScan][1]? [1]: https://www.ebi.ac.uk/interpro/ ...
written 2 days ago by Sej Modha1.7k
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Answer: A: How find variants between 26 genes sequence
... Checkout answer(s) on this thread: https://www.biostars.org/p/248564/ ...
written 3 days ago by Sej Modha1.7k
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Answer: A: Remove lines if duplicated values in column 1 has specific condition for column
... Simple bash sort solution: sort -k1,1 -k2,2nr test_file | sort -u -k1,1 ...
written 3 days ago by Sej Modha1.7k
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Answer: A: Ribo-seq rRNA and other contaminants Fasta file for S. pombe
... I am not sure about the specific organisms but it'd be worth looking at SILA rRNA databases: https://www.arb-silva.de/ ...
written 13 days ago by Sej Modha1.7k
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Comment: C: Error in fetching the Refseq using Taxonomic ID
... I don't think a document like that exists. @Joseph Hughes had asked a similar question: https://www.biostars.org/p/199261/. I tend to use the NCBI web pages to tackle such complicated queries in GUI first and then try to recreate those links using eutils and bit of help from https://www.ncbi.nlm.nih ...
written 13 days ago by Sej Modha1.7k
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Comment: C: Error in fetching the Refseq using Taxonomic ID
... That's right, you will need another filter that fetches the representative assembly. Following command returns fasta sequence for NC_000962.3. esearch -db genome -query "txid1438843[Organism]"|elink -target assembly|efilter -query "representative[PROP]"|elink -target nuccore -name assembly_nuc ...
written 13 days ago by Sej Modha1.7k
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Answer: A: Error in fetching the Refseq using Taxonomic ID
... I was able to download the sequences by removing the space between `txid1438843` and `[Organism]` esearch -db genome -query "txid1438843[Organism]" | elink -target nuccore | efilter -query "refseq"|efetch -format fasta ...
written 14 days ago by Sej Modha1.7k
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Comment: C: Python library for parsing bcftools stats file
... https://pyvcf.readthedocs.io/en/latest/ ...
written 15 days ago by Sej Modha1.7k

Latest awards to Sej Modha

Teacher 1 day ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Appreciated 3 days ago, created a post with more than 5 votes. For A: NCBI Protein GI to Genome Accession
Good Answer 3 days ago, created an answer that was upvoted at least 5 times. For A: NCBI Protein GI to Genome Accession
Scholar 3 days ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Scholar 13 days ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Where is the source code for legacy BLAST?
Appreciated 6 weeks ago, created a post with more than 5 votes. For A: NCBI Protein GI to Genome Accession
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: Where is the source code for legacy BLAST?
Scholar 8 weeks ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: NCBI Protein GI to Genome Accession
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Where is the source code for legacy BLAST?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Where is the source code for legacy BLAST?
Student 3 months ago, asked a question with at least 3 up-votes. For 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
Teacher 3 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: Where is the source code for legacy BLAST?
Guru 6 months ago, received more than 100 upvotes.
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Where i can find complete genome of any organism?
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Where i can find complete genome of any organism?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Where is the source code for legacy BLAST?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Remove duplicate protein sequences having different fasta identifiers
Scholar 8 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file

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