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FelixKrueger / Bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states
http://felixkrueger.github.io/Bismark/
GNU General Public License v3.0
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deduplicate_bismark problem #691

Closed iranianuser closed 3 months ago

iranianuser commented 3 months ago

hello again

I used deduplicate_bismark and I got these results:

Total number of alignments analysed in SRR4298802_1_val_1_bismark_bt2_pe.bam:   134138868
Total number duplicated alignments removed: 2279406 (1.70%)
Duplicated alignments were found at:    2212334 different position(s)

Total count of deduplicated leftover sequences: 131859462 (98.30% of total)

what was wrong with my process? my reads are PE (WGBS) and RG hg38

Thank you for answering my questions patiently

FelixKrueger commented 3 months ago

Why would you assume that anything is wrong with your process? This looks like a well diverse library.

iranianuser commented 3 months ago

oh! really??? I'm so glad to hear that :)

I'm thankful for your response

iranianuser commented 3 months ago

well I thought there must be at least some duplicated alignments removed

FelixKrueger commented 3 months ago

Well:

Total number duplicated alignments removed: 2279406 (1.70%)

That's not nothing?