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Recent Replies
Comment: Mouse or Rat Gene Expression Data Similar to GTEx
by
GenoMax
142k
Past thread: https://www.biostars.org/p/178266/
Answer: Mouse or Rat Gene Expression Data Similar to GTEx
by
GenoMax
142k
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
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
by
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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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
by
Pierre Lindenbaum
162k
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
Answer: merge overlaps and remove non overlap genomic windows
by
Pierre Lindenbaum
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> have two bed files
these are not bed files. A chromosome is missing in chromosome 1
> How can I create a file from the two mention…
Comment: Small secondary peak for per sequence GC content - FASTQC results (bulk RNA-seq)
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GenoMax
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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 …
Comment: Allele count of 2 for homoplasmic MT variants in VCF
by
GenoMax
142k
Please accept the answer (green check mark) to provide closure to this thread.
Comment: Trimmomatic running but files containing purged reads are empty
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GenoMax
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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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Arton
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Thank you for the helpful answer!
Comment: How to get the ratio of allele counts from GATK derived VCF file?
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DBScan
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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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