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Recent Replies
Comment: error in extracting one chromosome from multiple fasta files to a single fasta f
by
evafinegan
•
0
Thank you! All the fasta files do not have the same prefix as "sample". So, based on your suggestion, I tried
for S in *fasta.gz ; do …
Answer: How to add missing residues using swissPDBviewer
by
Mensur Dlakic
★
11k
SwissPDB viewer is not appropriate for this purpose. Most likely you don't need to add the missing residues, unless you have a reason to be…
Comment: error in extracting one chromosome from multiple fasta files to a single fasta f
by
Pierre Lindenbaum
135k
for S in 1 2 ; do samtools faidx "sample${S}.fasta.gz" "sample${S}_rhg1.0ch1" ; done > all_ch1.fasta
Comment: error in extracting one chromosome from multiple fasta files to a single fasta f
by
evafinegan
•
0
Yes, I checked that the
> `ch1` is `sample1_rhg1.0ch1` in `sample1.fasta.gz` and
`ch1` is
> `sample2_rhg1.0ch1` in `sample2.fasta.gz`
…
Comment: error in extracting one chromosome from multiple fasta files to a single fasta f
by
Pierre Lindenbaum
135k
there is no ch1 in your fasta file.
check this with
grep -F -w ch1 *.fai
just look at the fai files to find the correct name.
Comment: ATAC-seq fragment length distribution wrong but data makes sense!
by
ATpoint
49k
> How big a deal is the fragment distribution in terms of QC of the data?
I'd say the most important one together with the number of peaks…
Answer: computing multiple PRS on the fly with plink
by
chrchang523
8.0k
plink 2.0 has a [--score-col-nums][1] flag that lets you compute multiple scores at a time.
[1]: https://www.cog-genomics.org/plink/…
Comment: GSVA R packages
by
Kevin Blighe
73k
Hello, if you wish to use "*Poisson*", then you should use `counts(dds, normalized=TRUE)`
Comment: PLINK: ERROR: No nonmissing markers for individuals when using --cluster
by
chrchang523
8.0k
1. You aren't accurately reporting the commands you ran. `plink --file data.vcf ...` won't work after `vcftools --vcf data.vcf --plink --o…
Comment: Batch correction on scRNA-Seq data
by
elb
▴
200
So basically it is biological heterogeneity that as far as I know is a source of variability that should be corrected as the technical nois…
Comment: error in extracting one chromosome from multiple fasta files to a single fasta f
by
evafinegan
•
0
Thank you, Pierre! I tried and it gives an error:
[W::fai_get_val] Reference ch1 not found in FASTA file, returning empty sequence
…
Answer: error in extracting one chromosome from multiple fasta files to a single fasta f
by
Pierre Lindenbaum
135k
your running a command line like
samtools faidx *fasta.gz ch1 > all_ch1.fasta
so if you have multiple fasta.gz file in the direc…
Comment: EQTL FDR vs raw p-value
by
Carlo Yague
6.0k
> For some variants the FDR is lower than the p-value and for others the
> other way around (does this mean sth.?)
Isn't that impossible ?…
Comment: Impute variants with the PHG. Pipeline and VCF final output for each sample
by
Miguel
▴
10
I ran the step 3E but The output VCF does not have any called genotypes for the sample as the relevant sample columns have a "." all the r…
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