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ATpoint
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Recent Replies
Comment: How can I open BAM files?
by
GenoMax
123k
Other options in: https://www.biostars.org/p/9546448
Comment: STAR solo segmentation fault after 'started Solo counting'
by
bp22
•
0
Hi ATpoint,
Thanks for your response.
I am running it on a system with 64GB memory and 2TB of storage.
Best,
BP
Comment: getting weird volcano plot
by
Ram
37k
https://www.biostars.org/u/72168/ Why did you delete this post?
Comment: How do I convert a DIAMOND .daa file into human readable format?
by
GenoMax
123k
This may be a question for the developer : https://www.biostars.org/u/35858/
Comment: STAR solo segmentation fault after 'started Solo counting'
by
ATpoint
66k
How much memory is available?
Comment: Extract UMIs using UMI-tools
by
Matthias Zepper
2.2k
In all fairness, I have to admit that this documentation didn't exist when this question was posted and also the pipeline didn't support `-…
Comment: Getting information on CRAM files from headers inside the files
by
GenoMax
123k
Thinking about this again, it may be safer to look for coverage rather than guess based on file names,.
Based on the @PG lines you includ…
Comment: ATAC-seq +4 -5 shift
by
shelkmike
▴
830
The link doesn't work. Could you please reupload the file?
Comment: The most efficient way to take several random reads from CRAM file?
by
Istvan Albert
95k
samtools can quickly fetch reads over an interval; thus, all you need is to generate these random intervals as a BED file:
Filtering o…
Comment: Creating a phylogenetic tree following MSA
by
Xylanaser
▴
80
i recommendusing linux and cmd :)
Answer: Creating a phylogenetic tree following MSA
by
Xylanaser
▴
80
Try this: https://www.megasoftware.net/downloads/dload_win_gui
Answer: Regarding genotype input format of mrMLM for GWAS analysis?
by
Dana
•
0
you can find the answer in the user manual of the [article][1] (File S3. User manual for mrMLM v4.0.2):
"genotype for code 1", indicate…
Comment: The most efficient way to take several random reads from CRAM file?
by
artemd
▴
10
It's not important to have it accurate, an estimate could be good enough. You have some specific tool in mind?
Answer: Annotate VCF with Pathways (without performing GSEA)
by
Pierre Lindenbaum
150k
download https://reactome.org/download/current/ReactomePathways.gmt.zip
extract the genes:
```
unzip -p saved.zip ReactomePathways.gmt |…
Answer: Header change in NCBI SRR files
by
Anda
▴
10
you can try this sed:
sed -i "s/ length=150//g ; s/ /-/g ; s/\./-/g" YOUR_FASTQ_FILE
explanation: first, space and the following **l…
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