User: User000

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User000380
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Posts by User000

<prev • 284 results • page 1 of 29 • next >
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Comment: C: Replace heterozygous GT to missing in vcf file using bcftools
... Hi, I'm using this command line: `/DATA/Tools/bcftools-1.10.2/bcftools filter -S . -e 'GT=="het"' {input.f1} > {output.f2}` It seems to be working...it that OK? because I expect -e to exclude, no? Should I run something like `/DATA/Tools/bcftools-1.10.2/bcftools filter -i 'GT=="het"' {input.f1} & ...
written 29 days ago by User000380
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Comment: C: Replace heterozygous GT to missing in vcf file using bcftools
... -i doesnt work, -e seems to be working, is it normal? ...
written 4 weeks ago by User000380
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Replace heterozygous GT to missing in vcf file using bcftools
... Hello, I would like to replace all `het GT 0/1` or `1/0`to missing data `./.` ? Is there any way to do it with `bcftools`? If no how could I do it. ...
vcf bcftools written 4 weeks ago by User000380
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Comment: C: It is possible to get gzipped fastq.gz files as output in SABRE?
... I did something and nevertheless the errors the program build sabre executable, and the files it creates are `gzip compressed data, from Unix`.But I am not sure the changes I made to the script are OK. Could you, please, check? Should I create a new question? Thank you ...
written 6 weeks ago by User000380
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Comment: C: It is possible to get gzipped fastq.gz files as output in SABRE?
... Since nothing was happening I re-build by typing `make` and it gave the following error (I put only a piece because it is too long for a comment): gcc -Wall -pedantic -DVERSION=1.00 -O3 -c src/demulti_single.c src/demulti_single.c: In function ‘single_usage’: src/demulti_single.c:28 ...
written 6 weeks ago by User000380
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Comment: C: It is possible to get gzipped fastq.gz files as output in SABRE?
... Thanks so much! For now it is not working: should I change only il file `demulti_single.c`? also, `infn` will become `ingzn`? ...
written 7 weeks ago by User000380
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Comment: C: It is possible to get gzipped fastq.gz files as output in SABRE?
... OMG, update will be hard for me, I can try, but I am not a brilliant programmer :) thank you ...
written 7 weeks ago by User000380
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Comment: C: It is possible to get gzipped fastq.gz files as output in SABRE?
... I see, so I will have to gzip them post-demultiplexing. But it actually supports the gzip input, right? As stated also in the documentation "Sabre also supports gzipped file inputs" . Thank you a lot ...
written 7 weeks ago by User000380
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It is possible to get gzipped fastq.gz files as output in SABRE?
... Hello, A quick question. I am using [SABRE][1] to demultiplex my single end GBS `fastq.gz` files. As input I am using directly my gzipped `fastq.gz` files, but I am not getting the output as a gzipped `fastq.gz`. Sabre is instead outputting a normal `ASCII text`, so `fastq` file. Is there any way t ...
demultiplex sabre written 7 weeks ago by User000380 • updated 7 weeks ago by Pierre Lindenbaum129k
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Comment: C: Bedtools intersect with header file
... I actually solved the problem 4 months ago I guess, so I do not remember now what was the problem, but it was pretty easy at the end :) and I never said it does not work ...
written 7 weeks ago by User000380

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