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Recent Replies
Answer: samtools idxstats not removing ChrM
by
Jen
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![enter image description here][1]
I think I got it to work using "MT" rather than "ChrM" (code below)
samtools idxstats chipse…
Answer: how to get pfam id of proteins belonging to a particular family along with seque
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GenoMax
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Visit: https://www.uniprot.org/uniprotkb?query=(taxonomy_id:9606)
Click on `customize columns`. Search with keyword `pfam` and check the…
Comment: how to get pfam id of proteins belonging to a particular family along with seque
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Pierre Lindenbaum
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use the data in the download section ?
$ wget -qO - "https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/protein2ipr.dat.gz" …
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benformatics
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i think picard is expecting read groups. you may need to add them:
https://gatk.broadinstitute.org/hc/en-us/articles/360037226472-AddOrRepl…
Comment: samtools idxstats not removing ChrM
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benformatics
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i'm not sure this is doing what you expect?
you should try filtering your bam directly and then running idx stats
samtools view -h yo…
Comment: samtools idxstats not removing ChrM
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can we see the output from this?
`samtools idxstats chipseq/results/bowtie2/PPARg/PPARg_Input_Rep1_aln_sorted.bam`
conversely just as an e…
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It's bad practice to delete posts that received an answer ( = a user invested time - in this case me but it of course applies generally). D…
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EkHe
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Hi @juke34, if you're able, can you please clarify something for me (based on the answer you've given here)? Thanks a lot in advance. I als…
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FYI - The latest PHG docker version (tag 1.4) has a fix for this issue.
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Nextflow should only link inputs (unless stated otherwise), so even if you use outdir as input it should not be much of an issue, but still…
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Hi https://www.biostars.org/u/126271/,
welcome.
it might be good to add some more info on your "question". Now it only shows an error mes…
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Thank you for your answer
I'm using Ubuntu 22.04.2 LTS,
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Yes, don't use the outdir as an input. You might get infinite loops.
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I tried unzipped file, it shows the same error
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> use python package to load and analysis vcf.gz files
looks like it doesn't like gzipped file. Are you sure this software can read gzip…
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