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Flexbar could't identify Y base? #33

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HuaZou opened this issue Sep 10, 2020 · 0 comments
Open

Flexbar could't identify Y base? #33

HuaZou opened this issue Sep 10, 2020 · 0 comments

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@HuaZou
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HuaZou commented Sep 10, 2020

When I used this software to trim amplicon reads for 515F-806R primer, it reported the error as follows:

ERROR: Unexpected character 'Y' found.
Program execution aborted.

the following are the shell command and the primer sequance:

  • command line
flexbar -a illumina_PE_adapter.fa   \
-ao 5 \
-qt 30    \
--min-read-length 180  \
 --threads 2  \
 --zip-output GZ \
 --max-uncalled 10   \
 -r /disk/user/zouhua/project/Hypertension_16s/Study/00.RawData/HTN1/FDMP20H002931-1a_L1_HTN1.raw_1.fq.gz \
 -p /disk/user/zouhua/project/Hypertension_16s/Study/00.RawData/HTN1/FDMP20H002931-1a_L1_HTN1.raw_2.fq.gz \
  --target result/02.trim/HTN1  \
2>result/logs/02.trim/trim_HTN1.log
  • primer sequence
>forward_sequence_515F
CCTAYGGGRBGCASCAG
>reverse_sequence_806R
GGACTACNNGGGTATCTAAT

So I wonder that whether flexbar is suitable on trimming primer sequence ?

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