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jhhung / PEAT

An ultra fast and accurate paired-end adapter trimmer that needs no a priori adapter sequences.
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peat_report.txt does not explain enough #23

Closed tseemann closed 9 years ago

tseemann commented 9 years ago

The new peat_report.txt is good but it does not explain enough.

Can you let us know which adaptor sequences were common and trimmed? Or k-mers? Something so we can figure out what it was.

Maybe output the trimmed sequenced to peat_discarded.fq ?

RalfHsiao commented 9 years ago

We added the option --adapter_contexts in new release v.1.2.2 to output the adapter contexts. Thank you for your advice.

tseemann commented 8 years ago

Can you please explain what the numbers "2" and "1" mean? Are they for R1 and R2 reads?

The top numbers of adpater contexts:
Context Number
TTACGACCATGTCGTTCACA    2
TTTTG   1
TGAG    1
TG      1
TCTCTTTATTAGCCATTTGTTCTTGA      1
T       1
GGAACTTTCGAGGGG 1
GCTCCTAAGTCTC   1
GATCATTGCATGATCAGCCACGTGATCAGTGCATGATATCCACGTGATCAG     1
CTTCTCTTTATTAGTCATTTGCTTTTCAGG  1

Can you tell us how many reads matched each adapter context?

Does it make sense that T is an adaptor context?

RalfHsiao commented 8 years ago

The number "2” is the adapter number. The number was aggregated by R1.

Torsten Seemann notifications@github.com 於 2015年11月20日 上午10:31 寫道：

Can you please explain what the numbers "2" and "1" mean? Are they for R1 and R2 reads?

The top numbers of adpater contexts: Context Number TTACGACCATGTCGTTCACA 2 TTTTG 1 TGAG 1 TG 1 TCTCTTTATTAGCCATTTGTTCTTGA 1 T 1 GGAACTTTCGAGGGG 1 GCTCCTAAGTCTC 1 GATCATTGCATGATCAGCCACGTGATCAGTGCATGATATCCACGTGATCAG 1 CTTCTCTTTATTAGTCATTTGCTTTTCAGG 1 — Reply to this email directly or view it on GitHub https://github.com/jhhung/PEAT/issues/23#issuecomment-158261441.