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Recent Replies
Comment: Very low successfully assigned alignments with feature counts
by
GenoMax
136k
Is the genome/annotation from the same source i.e. Ensembl or so it appears?
Comment: Calculate GC content for entire chromosome
by
ATpoint
78k
What does this do? It's not documented well and does not work for me in terms of, it produces no output:
cat foo.fa
>chr1
GCGC…
Comment: Need help to find FASTA sequence from dbSNP
by
GenoMax
136k
Did you not see the last part in my comment above about how to get the sequence?
Comment: Need help to find FASTA sequence from dbSNP
by
syedahumairagillani
•
0
Thank you for your response.
Actually I am looking for fasta sequence of SNP as I shared via image, rather than just location. Would you p…
Answer: Calculate GC content for entire chromosome
by
colindaven
5.8k
In the meantime there is also
seqtk gc
https://github.com/lh3/seqtk
seqtk gc
Usage: seqtk gc [options] <in.fa>
…
Comment: Building reference dbSNP file using WGS samples
by
analyst
▴
10
I have employed your above suggested approach for BQSR (latter one).
I will try former approach too (that does not require reference vcf fi…
Comment: An issue with gtf file (ballgownrsem)
by
cucindarko51
•
0
Thank you! After using this tool, I figured out that **ballgownrsem** can be run successfully only with GFF files.
Answer: Execute R command on specific termimal
by
ATpoint
78k
This is not how HPCs work. Things do not happen automatically and independent of the job scheduler.
If you want to work interactively o…
Comment: Need help to find FASTA sequence from dbSNP
by
GenoMax
136k
Using [**EntrezDirect**][1] you can find the location of this SNP:
$ esearch -db snp -query rs1815739 | esummary | xtract -pattern Doc…
Comment: Building reference dbSNP file using WGS samples
by
analyst
▴
10
For variant calling I followed following steps:
**Step 1**
I first made a vcf file to be used for quality score recalibration later
> c…
Answer: How to use Nextflow to call scripts from different environments?
by
ATpoint
78k
You can specify conda environments and containers directly in the modules, see for example:
https://github.com/nf-core/modules/blob/master…
Comment: Issues while running blastx
by
GenoMax
136k
> ~/Downloads/uniprot_sprot.dat
`dat` files are not blast index ready. You should download the `fasta` format file and create your own bla…
Comment: Strandedness of RNA-seq results
by
charles.feigin
•
0
Hi, coming here for the same reason. Libraries prepared with the Illumina Stranded mRNA Prep kit (dUTP-based).
In hisat2 with --rf I get <…
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