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Recent Replies
Comment: Flag multiple filtering steps on VCF files using VEP
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I don't understand that question.
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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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sorry i edited my example. But your answer is exactly the opposite of what I want
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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.
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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.
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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…
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> Why is trimmomatic not removing any reads?
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Since a specific region is being amplified it is expected that many of the library fragments will have identical sequences. Thus the low nu…
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@genomax Thank you so much for replying. I was quite unsure about the qualities. One more question. There is no problem within nucleotide d…
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