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Recent Replies
Comment: TCGA CNV data 1p/19q codeletion (whole arm deletion)
by
Kevin Blighe
73k
Excellent work - thanks. So, this information must have been in PanCancerAtlas clinical information. Noted for future!
Answer: Concatenating gmt files from msigdb
by
Kevin Blighe
73k
Hi, it is as if there is neither an end-line (`\n`) nor carriage return (`\r`) at the end of each line in each file. Perhaps you originally…
Comment: TCGA CNV data 1p/19q codeletion (whole arm deletion)
by
Isabelle
•
0
Hi Kevin, thanks a lot for your kind reply.
I finally find a way to download the IDH mutation status and 1p/19q codeletion status of TCGA-G…
Comment: vcftools 012 output missing homozygous minor genotype
by
tkloppe
•
0
I encountered the same problem with a gvcf file called with GATK on haploid genome samples.
I only find “-1” for missing data which makes…
Comment: adjusted p-values in meta-analysis
by
kindisha_blue4
•
0
Thank you very much for your time and help! I will take a look at the other packages (although in principle **metafor** is the package used…
Comment: Comparing two variant files
by
prasundutta87
▴
480
I agree. Adding information like gene names/trascript ID/exon, etc. is helpful when you have two files with variants annotated by two diffe…
Comment: How get density plot TSS region for genes of interest
by
BISEP
•
0
@jared.andrews07 Can convert my GTF file to bed file, and get the genes what I wanted and run the computeMatrix, TSS region I can run What …
Comment: How to change color of rownames display in pheatmap
by
jared.andrews07
9.6k
Please open up a new question and post your full code, resulting image, and what you hope to achieve. Piggybacking on questions tends to cl…
Comment: How get density plot TSS region for genes of interest
by
jared.andrews07
9.6k
Yes, see the usage example on that page. You'll have to run `computeMatrix` with a bed file containing each of your genes along with bigwig…
Comment: Varying length sequences in hhblits (hhsuite 3.3) generated MSA
by
sajid
•
0
Thanks a lot. `reformat.pl -M first -r a3m a3m` did it for me. Initially reformat messed things up even more until I added `-r` to the comm…
Comment: BLASTX script doesn't print results and never ends
by
Mensur Dlakic
★
11k
Just realized that a near-identical question of yours was already answered [**here**][1]. Since that answer was accepted, I assumed that it…
Answer: BLASTX script doesn't print results and never ends
by
Mensur Dlakic
★
11k
Chances are that you haven't waited long enough because I am guessing that your query file is large, and it is obvious that you have a larg…
Comment: Error in running miRDeep2
by
Ram
33k
If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more t…
Comment: Comparing two variant files
by
Ram
33k
To add to https://www.biostars.org/u/37063/'s comment, if you can create an ID out of CHROM, POS, REF and ALT, you won't need any other fie…
Comment: Comparing two variant files
by
prasundutta87
▴
480
As mentioned by many people here, BCFtools isec is a good way, but you need a VCF file for that.
There is another way which can utilise y…
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