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Ram
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David Langenberger
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6
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6
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8.4k
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Ram
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written 9.0 years ago by
David Langenberger
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6
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3.7k
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updated 5 weeks ago by
Ram
38k
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written 10.2 years ago by
David Langenberger
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Rainer
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130
9
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6
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1
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updated 10 weeks ago by
synat.keam
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70
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written 3 months ago by
carlopecoraro2
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updated 3 months ago by
Ram
38k
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updated 28 days ago by
Ram
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Ahmed Youssef
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Ram
38k
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97k
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5
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Comment: Total No of Genes of GENCODE Release 43
by
ahmad
•
0
Thank you, its correct.
In my code I was using (https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_43/gencode.v43.primary_as…
Answer: extract gene coordinates and TSS from gene list
by
Gordon Smyth
★
5.6k
To get gene bodies:
```
library(Rsubread)
GeneBody <- promoterRegions("mm10", upstream=0, downstream=Inf)
```
To get TSS +/- 1000 bp:
```
T…
Answer: find the mate of a read using pysam
by
Walter
•
0
I just came across this problem, and this is the solution I'm using right now. I'm sharing it here as it is one of the first and most recen…
Comment: best pipeline/practice for analyzing WES for germline and somatic variant callin
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epigene
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i meant i've never used it myself.. :p
Comment: best pipeline/practice for analyzing WES for germline and somatic variant callin
by
Pierre Lindenbaum
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new ? happy birthday nextflow :-)
https://twitter.com/nextflowio/status/1638557822509088772
Comment: best pipeline/practice for analyzing WES for germline and somatic variant callin
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epigene
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Pierre, could you please also recommend some well validated fastq file sets to test the pipeline and compare with other callers? I've known…
Comment: best pipeline/practice for analyzing WES for germline and somatic variant callin
by
epigene
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thanks for sharing! looks a new pipeline tool to learn..
Answer: best pipeline/practice for analyzing WES for germline and somatic variant callin
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Pierre Lindenbaum
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https://nf-co.re/sarek
> nf-core/sarek is a workflow designed to detect variants on whole genome or targeted sequencing data. Initially …
Answer: ORA analysis (over-representation analysis) : different package different padjus
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chaco001
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This could be due to a few different things.
1. It isn't completely clear from your example whether `id` and `genes` are the same list,…
Comment: How can I use bcftools mpileup or an alternative to find ALL variants without an
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chaco001
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Thanks for your reply. The problem is the output from `mpileup` doesn't contain the deletions, so neither will `call`.
Comment: Align miRNA library (small RNA-seq) without trimming
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Paola
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Hi
Thank you for lettig me know. I was seeing that others also sets the minimum lenght 18bp for miRNA analysis. And I agree that I should…
Comment: Align miRNA library (small RNA-seq) without trimming
by
Buffo
★
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> It seems that untrimmed are beneficial regarding alingment and
> computational time consuming.
There is no benefit if your reads have ad…
Answer: ORA analysis (over-representation analysis) : different package different padjus
by
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Don't worry about it, those p-value and q-values in these tools are mostly "make-believe".
The problems with ORA analyses are so profou…
Answer: extract gene coordinates and TSS from gene list
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Trivas
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I always like using the UCSC Table Browser for things like these. You might need to convert to Refseq (NM_*) for it to work well, which can…
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by
Usama
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Thank you very much for your suggestion.
My question is I have used MACS2 to get the peaks, the output files of macs2 are:
-sample.lambda.b…
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