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Recent Replies
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
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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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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…
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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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Arton
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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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Thank you GenoMax!
So would we just prepare the dual-indexed library and ask the sequencing service to do single-end sequencing?
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Hi Anitha, you can take inspiration from here on which data to use and how to set up your WGS circle plot.
[https://www.tandfonline.com/…
Comment: Trimmomatic running but files containing purged reads are empty
by
Wilber0x
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Thanks for the advice, it seems like it is likely I have the incorrect adaptor sequences, though I am still surprised that no low quality r…
Answer: Trimmomatic running but files containing purged reads are empty
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> Why is trimmomatic not removing any reads?
It is not mandatory that your data have extraneous/adapter sequence. If no extraneous sequenc…
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