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Comment: R, group data based on names and sum each group
by
cpad0112
20k
with R
library(dplyr)
df %>%
group_by(col4,col5) %>%
mutate(sum=sum(col6)) %>%
ungroup()
> with (df, agg…
Comment: GSEA not returning significant gene sets
by
cpad0112
20k
how does the PCA of the normalized counts look? can you see the grouping of samples as per metadata/variables?
Comment: error while using cyvcf2 to parse the vcf file
by
rheab1230
▴
50
I checked with the above command and it seems like my vcf file is broken:
bcftools view chr22_id1.vcf > /dev/null && echo "OK"
…
Answer: Adding a new protein to similarity matrix based on sequence alignment
by
Mensur Dlakic
★
19k
In short: you can't go wrong by re-aligning, and it is possible to go wrong by concocting some kind of similarity matrix without re-alignin…
Comment: Using fastq-mcf tool
by
Ram
36k
I'm sure this has been mentioned to you before (and your post before editing shows you know how to do it), please format code as code where…
Answer: Using fastq-mcf toolk
by
Pierre Lindenbaum
145k
your trying to run the **manual** file ( https://linux.die.net/man/1/intro ) of your tool (`fastq-mcf.1`), not the executable itself
there…
Comment: error while using cyvcf2 to parse the vcf file
by
Pierre Lindenbaum
145k
if the command
bcftools view chr22_id1.vcf > /dev/null && echo "OK"
prints OK and shows no error, then it's a problem with cyvcf2
ot…
Comment: Long variant splits to several variants by variant callers
by
vdauwera
★
1.2k
To troubleshoot that sort of thing, you need to re-run HaplotypeCaller with the -bamout argument so you can see what it was "thinking". If …
Comment: error while using cyvcf2 to parse the vcf file
by
Pierre Lindenbaum
145k
thanks it *does* look like a vcf.
Comment: blast with multithreads is much slower
by
biobiu
▴
130
Of course.
Things went slow with one thread so I hoped to speed things up a little bit with multithreading.
The surprise was not from not …
Comment: Error in GATAK haplotypecaller running
by
Ram
36k
I've changed that tag to GATK. It probably was a language barrier thing.
Comment: error while using cyvcf2 to parse the vcf file
by
rheab1230
▴
50
The only difference is the ID column; I had to edit the ID column with this format `chr22_16062270_G_T_b37` to do further analysis.
Comment: error while using cyvcf2 to parse the vcf file
by
rheab1230
▴
50
for command3:
grep "#CHROM" -C2 chr22_id1.vcf
##bcftools_annotateVersion=1.13+htslib-1.13
##bcftools_annotateCommand=annotate -c …
Comment: error while using cyvcf2 to parse the vcf file
by
rheab1230
▴
50
I have added the output for the above command:
for command (1):
file chr22_id1.vcf
chr22_id1.vcf: ASCII text, with very long lines
…
Comment: Error in GATAK haplotypecaller running
by
Pierre Lindenbaum
145k
what is this tag "hannah" ?
did you read https://gatk.broadinstitute.org/hc/en-us/articles/360035531652-FASTA-Reference-genome-format
>…
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