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Recent Replies
Comment: Different output for read length
by
GenoMax
142k
Post the data at pastebin.com and add a link here or you could a GitHub gist. You were suspended by biostars SPAM bot since you pasted link…
Comment: Different output for read length
by
GenoMax
142k
Post the data at pastebin.com and add the link here. You were suspended by biostars SPAM bot since you pasted these links in quick successi…
Comment: RNA seq analysis
by
s.ghazala
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0
Could you clarify on what exactly you are referring to with "SRA data table". If you are retrieving fastq files (raw data), then you could …
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
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sovrappensiero
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Thanks, Chris. I really appreciate your help. This has clarified a lot for me!
Answer: Snakemake fails to find conda in PBS
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tim.booth
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Snakemake does not have support for micromamba. There is an open issue: https://github.com/snakemake/snakemake/issues/2322
Comment: absolute path for symbolic links in Snakefile
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tim.booth
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Further to this answer - if you are using GNU coreutils (ie. any modern Linux), there is a "-r" flag to fix this problem. I typically use "…
Answer: Different output for read length
by
Pierre Lindenbaum
161k
I supect your reads are hard clipped. Show us the first lines of
samtools view /home/sorted.bam | cut -f 2,6,10 | head -n 20
Comment: Presence of unknown sites in ANNOVAR output file
by
sainavyav22
•
0
Here you go.
1.perl convert2annovar.pl -format vcf4old 1008_Tumor.vcf > 1008Tumor_variant.avinput
2.perl annotate_variation.pl 100…
Comment: Filtering Multi-sample VCF file for all except one Genotype
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Jeremy Leipzig
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Those are samples. If a sample has a 0/1 or a 1/1 genotype for that variant, they have the variant.
Your question is ambiguous because you…
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> That turns it into a mess of paragraphs
See above. Select (highlight with mouse) the part you want to represent as `code` and then click…
Comment: Help with Biopython for Beginner
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cput
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That turns it into a mess of paragraphs, but if it truly is more productive thanks for the tip!
Comment: Presence of unknown sites in ANNOVAR output file
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Ram
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Please show us your full annovar command line.
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I've done what I can to make your post more professional. Stick to outlining your problem, personal pleas do not really belong on a profess…
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rackbersingh
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Hi Phillip,
Thanks for providing an answer and clearing up some confusion, looking into what you said about older assemblers reverse comp…
Comment: How to analyze Infinium Mouse Methylation BeadChip array data?
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Tawny
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Did you get this figured out? I am having the same error in R.
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