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Recent Replies
Answer: Extract first and last column of fasta-header
by
Hugo
▴
360
You can use the "Rename header / Multipart header" operation of SEDA (https://www.sing-group.org/seda/manual/operations.html#multipart-head…
Answer: cram to fastq
by
ATpoint
62k
Yes, either sort or collate (collate=group by name). Sort takes longer, so I would simply use `samtools collate` and feed the output into `…
Comment: Hardy-Weinberg equilibrium analysis in Plink for association study.
by
Nai
▴
20
Dear Pedro,
I don't have vcf file. I have case and control with growth parameters, rsid, chrom, position. I know the steps like QC which s…
Answer: cram to fastq
by
Pierre Lindenbaum
146k
form the samtools manual:
> The input to this program must be collated by name.
> Run 'samtools collate' or 'samtools sort -n' to achie…
Answer: Converting GP field in a VCF to GT
by
Garan
▴
680
After abit more digging around, I found the following solution:
QCTool
qctool -g input.vcf.gz -threshold 0.9 -og output.gt.vcf.gz…
Comment: R can install .zip package but not .tar.gz package
by
Basti
▴
460
What is the package you are trying to install ? DO.db is a bioconductor package, you may need `BiocManager::install("DO.db")`
Comment: all coding regions .bed file hg38 Whole Genome Sequencing
by
hdjc90
•
0
Apologies, I thought it was related as I imagined this is exactly what @cocchi.e89 was trying to do with the .bed file he was requesting.
Answer: volcano plot display selected labels
by
Kevin Blighe
81k
Hi, please can you do 2 things to resolve this:
- verify that all of the desired genes are in `dgeList_cpm_filtered_gtf$gene_name`
- us…
Comment: Quick download of FASTQ
by
Friederike
8.4k
Maybe you want to edit your question and its header to make clear that you're looking for support with Aspera?
Answer: How to ensure all fonts are written in Arial?
by
Friederike
8.4k
Just in case other users happen to encounter similar issues, here are my five cents on the topic:
Looking [at the `EnhancedVolcano()` co…
Answer: Quick download of FASTQ
by
lieven.sterck
14k
What I usually do is to go via [sra-explorer.info][1] , that site is excellent to search for datasets and to then get several options on ho…
Comment: Quick download of FASTQ
by
Carambakaracho
★
3.0k
Not a direct reply to your question: maybe you can give [gget][1] a try? I never tried it, and I'd be surprised if it was a drop in replace…
Answer: Why does the CADD database have multiple lines for the same mutation/substitutio
by
tomas4482
▴
140
This variant is a downstream variant of ENSG00000274697, annotated by Ensembl-VEP.
Comment: Align short sequence against ONT reads
by
kirillkirilenko.tomsk
•
0
Thank you I'll try this approach!
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