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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 "…
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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
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sainavyav22
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Here you go.
***1.perl convert2annovar.pl -format vcf4old 1008_Tumor.vcf > 1008Tumor_variant.avinput
2.perl annotate_variation.pl 1008Tumo…
Comment: Filtering Multi-sample VCF file for all except one Genotype
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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…
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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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Hi Phillip,
Thanks for providing an answer and clearing up some confusion, looking into what you said about older assemblers reverse comp…
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Did you get this figured out? I am having the same error in R.
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Try this:
```r
#Read the motifs
library(JASPAR2024)
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It's not possible. Gene counts are a region aggregate, bigwigs are a per-base readout and you cannot use normalized counts for mentioned to…
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> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: bcftools - reducing to "sites-only"?
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Matthew
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Thank you Pierre!
Not sure why I didn't notice that (I should have)
Comment: How to convert normalized BigWig file to count matrix?
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Pierre Lindenbaum
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bigwig is chrom/start/end/value . what kind of matrix do you want ?
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