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a.zielezinski
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rbronste
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Recent Replies
Comment: How to know the genome indices from STAR is correct
by
GenoMax
118k
I was asking you for the `tail` output of the `Log.out` file for index creation. Looks like you probably ran the alignment in the same dire…
Comment: GATK's selectVariants not outputting VCF
by
brunobsouzaa
▴
740
Your command seems incomplete... Try using with `--select-type-to-include INDEL`
If it works, you can use `--select-type-to-include` multi…
Comment: How to know the genome indices from STAR is correct
by
Chris
•
0
Yes, I am on macOS and I am surprised when I type period here, it was converted to a question mark.
tail -n 6 Log.out
Number of fastq fil…
Comment: How to know the genome indices from STAR is correct
by
GenoMax
118k
These files look to be about the right size when I compare them (for qualitative reason) so I am going to hazard a guess that the index sho…
Comment: LInear Models with HLA-B alleles in R
by
LChart
▴
320
The estimates are accurate in both cases, but as you say, the questions are different. It is fairly common for contrasts of the second form…
Comment: How to know the genome indices from STAR is correct
by
Chris
•
0
I run STAR by submitting the script so maybe the error if exists, it won't show as run directly from the shell.
-rw-r-----. 1 doanc2 doan…
Comment: SQL query to find all specific value in all columns based on row id.
by
Pierre Lindenbaum
147k
show us the schema for your database
Comment: LInear Models with HLA-B alleles in R
by
schagas
•
0
Thanks @lchart ! So would the second approach be a loss in the "accuracy" of the estimates?
And Anyway, the two ways are not wrong, sinc…
Comment: Comparison between two sets of cell lines
by
Vincent
•
0
Hi indolefin,
I am currently working on the same kind of question/hypothesis that you had. Did you find a tool to compare your groups of c…
Comment: How to know the genome indices from STAR is correct
by
GenoMax
118k
Are you sure the genome generate job completed successfully i.e. there were no errors? Can you show a listing of the files above so we can …
Comment: How I do lift over a Plink bim file from Hg18 to Hg19.
by
pabe
▴
10
Are you all using python2 or python3? Make sure it is python2. The liftOverPlink.py and rmBadLifts.py scripts will not work properly unless…
Comment: How to know the genome indices from STAR is correct
by
Chris
•
0
Creating genome indices took less than 1 hour with the output I listed above but the alignment is less than 1 minute so as you said there w…
Comment: How to filter out the promoter-TSS peaks from the `.narrowPeak` file?
by
LChart
▴
320
If your narrowPeak file has peak IDs in the NAME field you can
`awk '$8 == "promoter-TSS"' x.annot | cut -f1 > peak_names.txt'`
`grep -Wf…
Comment: How to know the genome indices from STAR is correct
by
GenoMax
118k
Indeed. This is about "genomegenerate".
Comment: How to know the genome indices from STAR is correct
by
GenoMax
118k
> Then I run alignment but the size of all output files is 0.
You are not running an alignment just yet. A `STAR genomegenerate` job can t…
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