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jdidion / atropos

An NGS read trimming tool that is specific, sensitive, and speedy. (production)
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trim nextera adapters #77

Closed lmanchon closed 5 years ago

lmanchon commented 5 years ago

--Hi,

i'm beginner in trimming sequence and i need somebody help in trimming Nextera adapters. My libraries are built in paired-end (2x150bp) mode using Nextera XT kit with those adapters:

PrefixNX/1 AGATGTGTATAAGAGACAG PrefixNX/2 AGATGTGTATAAGAGACAG Trans1 TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG Trans1_rc CTGTCTCTTATACACATCTGACGCTGCCGACGA Trans2 GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG Trans2_rc CTGTCTCTTATACACATCTCCGAGCCCACGAGAC

which parameters i need to set to clean my reads ?

thank you so much --

jdidion commented 5 years ago

I'd split your adapters into separate fasta files for the fw and rv adapters. Then use 

-a file:fw_adapters.fa -A file:rv_adapters.fa
lmanchon commented 5 years ago

just that and no other parameters to consider ?

jdidion commented 5 years ago

You're free to read the documentation regarding the other available parameters: https://atropos.readthedocs.io/en/latest/.