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Old 06-19-2011, 04:11 PM   #1
Location: paris

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Default Paired-end Illumina RNA-seq adapter trimming

Does anyone can recommend a tool for Paired-end Illumina RNA-seq adapter trimming? Most of tools are for single-end sequence. I think if there a tools used for paired-end data.
The shortcoming of the single end tools:
1, The single end tools sometimes will make the paired-end data mess.
2, It does not consider paired-end information, if there is a tool for paired-end, such remove will be accurately.
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Old 06-20-2011, 01:14 AM   #2
Simon Anders
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Location: Heidelberg, Germany

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HTSeq has facilities useful for this.

You can write a little Python script like this:

import itertools
import HTSeq

in1 = iter( HTSeq.FastqReader( "mydata_1.fastq" ) )
in2 = iter( HTSeq.FastqReader( "mydata_2.fastq" ) )
out1 = open( "trimmed_1.fastq", "w" )
out2 = open( "trimmed_2.fastq", "w" )

for read1, read2 in itertools.izip( in1, in2 ):
   read1.trim_right_end( "ACGGTC" )
   read2.trim_left_end( "TTCGAC" )
   read1.write_to_fastq_file( out1 )
   read2.write_to_fastq_file( out2 )
I haven't tested the script, and you will have to adjust it to your needs, of course.

Note that you can make the trimming tolerant to read errors by either adding a second argument, giving the allowed fraction of mismatches, or using trim_right_end_with_quals, which accepts a maximum sum of mismatch qualities. See here and here for an explanation.
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Old 06-20-2011, 01:47 AM   #3
Location: paris

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Simon Anders,
Thanks for your reply.
Could you please also give an example how to trim 3' reads which have low quality? For example, set a cutoff value. Bellow this cutoff, the nucleotide will be trimmed.

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Old 07-20-2011, 06:31 PM   #4
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Take a look at "". It works on both single and paired-end reads.
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Old 11-17-2011, 06:40 AM   #5
Location: Paris

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Posts: 13

We have the same problem for paired-end of 100bp and sizing of 200 (fragment size) from Illumina GAIIx RNAseq. In many case we think we got an adapter in 3' that have been sequenced... we think that because the mapping is very bad in 3'. BUT we know that the Quality score is very good (Q> 30). The problem is the 3'end can contains just some bases from the adapter and not the complete sequence... when the list of adapter is known did you find a tool to solve this problem ?

Thanks, vb
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Old 03-28-2012, 09:22 PM   #6
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Default Trimmomatic

We are using Trimmomatic as it is able to do trimming and adaptor removal for paired-end reads. At first we tried fastx-toolkit but then we switched to trimmomatic as a better choice for paied-end samples.
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Old 09-23-2013, 06:21 PM   #7
Location: Los Angeles, CA

Join Date: Jul 2011
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Default skewer

You may also try skewer which is an adapter trimmer dedicated to Illumina paired-end data

Last edited by relipmoc; 09-23-2013 at 06:23 PM. Reason: title
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Old 11-18-2013, 12:54 AM   #8
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May i know from where to download skewer ?
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Old 01-05-2015, 08:48 AM   #9
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Hi saran.ela123

you can download it from here:
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