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Answer: how to get pfam id of proteins belonging to a particular family along with seque
by
GenoMax
126k
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
by
Pierre Lindenbaum
153k
use the data in the download section ?
$ wget -qO - "https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/protein2ipr.dat.gz" …
Comment: Problem in converting SAM to BAM file by DROP SEQ
by
benformatics
3.4k
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
by
benformatics
3.4k
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
by
Jeremy Leipzig
21k
can we see the output from this?
`samtools idxstats chipseq/results/bowtie2/PPARg/PPARg_Input_Rep1_aln_sorted.bam`
conversely just as an e…
Comment: Nextflow Stringtie: command not found Error
by
ATpoint
70k
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…
Comment: Converting an output de-novo transcriptome assembled with Trinity to a .gff3 fil
by
EkHe
•
0
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…
Answer: Practical Haplotype Graph -- Pathing Error
by
lcj34
▴
220
FYI - The latest PHG docker version (tag 1.4) has a fix for this issue.
Comment: Nextflow: No space left on device, process using output directory as input?
by
Maxime Garcia
▴
220
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…
Comment: Problem in converting SAM to BAM file by DROP SEQ
by
lieven.sterck
14k
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…
Comment: Trying to install Roary with Conda results in error message
by
tobiwan
•
0
Thank you for your answer
I'm using Ubuntu 22.04.2 LTS,
command line used: conda install roary. Or do you need a screenshot of the whole …
Comment: Nextflow: No space left on device, process using output directory as input?
by
colindaven
4.5k
Yes, don't use the outdir as an input. You might get infinite loops.
Comment: UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid
by
wangjincheng
•
0
I tried unzipped file, it shows the same error
Comment: UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid
by
Pierre Lindenbaum
153k
> 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…
Comment: Trying to install Roary with Conda results in error message
by
ATpoint
70k
This cannot be answered. Add your command line and operating system.
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