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Recent Replies
Comment: samtools write-index
by
LucisTheFather
•
0
```
-o alignment.sorted.bam##idx##alignment.sorted.bam.bai
```
This portion is to get .bai index, instead of .csi indexing. Although Idk th…
Comment: samtools write-index
by
LucisTheFather
•
0
Really appreciate your help Pierre!
I am a little bit confused btw. do you mean this:
```
rm -vf alignment.sorted.bam.bai
minimap2 -ax map-…
Comment: samtools write-index
by
LucisTheFather
•
0
Yeah, I did multiple split tests of my pipeline (just subset 400k rows of my fastq and run through my pipeline for quick tests)
and none of…
Comment: Which 1000 genomes 30x files should I use for imputation?
by
David-walson
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Hi there. Have you found any suggestions? I have alos been working on the 1KGP high coverage data, but i have no idea about how to use it p…
Comment: MAUVE: No gene annotations in Genbank file alignments
by
pramach1
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40
The same problem persists for me too. Running progressiveMauve on command line on bunch of gbk files. Mauve itself runs fine and I do see t…
Answer: Error when looping over multiple columns in a data frame in R
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First of all, you should use "tag.healthy" and "methods" instead of "tag.health" and "method". Also, optimal.cutpoints() wants X to be eit…
Comment: Mouse or Rat Gene Expression Data Similar to GTEx
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GenoMax
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Past thread: https://www.biostars.org/p/178266/
Answer: Mouse or Rat Gene Expression Data Similar to GTEx
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GenoMax
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Mouse bodymap samples : https://ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA375882%20&o=acc_s%3Aa
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bk11
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Here is the [RatGTEx][1]
[1]: https://ratgtex.org
Comment: Random Access remote BAM files
by
a.penatauber
•
0
Hi Lucas, I am looking for a similar functionality as I'm working with a large volume of CRAM files on S3, and downloading them whole would…
Comment: from CRAM to fastq
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ATpoint
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Yes, but I still think that with this syntax you get an uncompressed file, because samtools does not detect the gz suffix. Just take a `hea…
Comment: merge overlaps and remove non overlap genomic windows
by
reza
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300
Overlap of "Ch1 200 250" and "Ch1 150 220" is "Ch1 200 220", but I want to combine windows that have overlap. Thus, my goal is to combine …
Comment: Flag multiple filtering steps on VCF files using VEP
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Pierre Lindenbaum
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I don't understand that question.
Comment: merge overlaps and remove non overlap genomic windows
by
Pierre Lindenbaum
162k
> But your answer is exactly the opposite of what I want
oh I see. but i don't understand the logic why:
"Ch1 200 250" and "Ch1 150 220" …
Comment: merge overlaps and remove non overlap genomic windows
by
reza
▴
300
sorry i edited my example. But your answer is exactly the opposite of what I want
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