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Recent Replies
Comment: multiqc: group samples by population + boxplot ?
by
Pierre Lindenbaum
155k
It worked by parsing a first run of multiqc, extract the data from the sanitised data , create a SVG plot with R, include the SVG into a fi…
Comment: Solving environment: failed with initial frozen solve. Retrying with flexible so
by
Ahmed
▴
10
thanks, bro I get the solve of my problem by installing new environment and reinstalling samtools software again.
Comment: Solving environment: failed with initial frozen solve. Retrying with flexible so
by
Ahmed
▴
10
Thanks for telling me that, and i apologize for bad explanation because I am beginner user with the site!
Comment: amrfinder not working on loop?
by
Pierre Lindenbaum
155k
what is the output of the following commands:
ls -lah '/home/bvs/neelam/AMRFINDER_hypo/hypothetical_analysis/P_aeruginosa_RP73.fasta'
…
Comment: amrfinder not working on loop?
by
GenoMax
130k
> Cannot open file
> '/home/bvs/neelam/AMRFINDER_hypo/hypothetical_analysis/P_aeruginosa_RP73.fasta'
Looks like either the file path is in…
Answer: Solving environment: failed with initial frozen solve. Retrying with flexible so
by
Ram
39k
1. `bioconda` is a conda channel, not a command. I'm surprised it executes some sort of binary - what is the output of `alias bioconda` and…
Comment: Solving environment: failed with initial frozen solve. Retrying with flexible so
by
Ram
39k
Use proper tags - in your previous post, you pasted the question text in the tag field and here, your tag is `nothing`. Use relevant tags (…
Comment: no output from GATK CombineGVCFs
by
Pierre Lindenbaum
155k
> The number of gVCFs in the list has a hard limit
no, I don't think so. But if you have 10000 VCFs, you should combine 100x100 VCFS and …
Comment: novel miRNA naming(annotation)
by
kuttibiotech2009
▴
30
Do you have any idea about it?. I also want to do the same.
Answer: Identify similarly mapped reads in BAM/SAM?
by
Pierre Lindenbaum
155k
bedtools bamtobed -i in.bam | datamash -g 1,2,3 collapse 4
Comment: GISTIC from ASCAT
by
Hyper_Odin
▴
290
Also, I would like to add that we cannot use ASCAT output for GISTIC input...since GISTIC expects all the chromosomes in the input file eve…
Comment: GISTIC from ASCAT
by
Hyper_Odin
▴
290
Hi, Ram thanks for the help...I figured out the issue.
somehow I had duplicate files in the folder which caused the issue.
Answer: multiqc: group samples by population + boxplot ?
by
Phil Ewels
★
1.2k
You can't group and make boxplots as you describe, probably your best bet is to use the [highlight tool][1] in the report (especially if yo…
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