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Recent Replies
Comment: Mouse or Rat Gene Expression Data Similar to GTEx
by
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
Answer: Mouse or Rat Gene Expression Data Similar to GTEx
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Here is the [RatGTEx][1]
[1]: https://ratgtex.org
Comment: Random Access remote BAM files
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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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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
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reza
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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
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Pierre Lindenbaum
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> 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
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reza
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sorry i edited my example. But your answer is exactly the opposite of what I want
Answer: merge overlaps and remove non overlap genomic windows
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> have two bed files
these are not bed files. A chromosome is missing in chromosome 1
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Have you checked for presence of rRNA in the affected samples? That can be one possibility for these peaks.
In theory if you are aligning …
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Please accept the answer (green check mark) to provide closure to this thread.
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Perhaps there were no low quality reads either.
Comment: Allele count of 2 for homoplasmic MT variants in VCF
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Thank you for the helpful answer!
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I think GATK only counts informative reads in AD, do you have a DP field? DP should be closer what FreeBayes reports. You can also check GA…
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