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Old 03-01-2016, 12:04 PM   #1
Rahul shelke
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Location: Guwahati,India

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Default Fastx and Soapdenovo trans

Hello,

I have filtered my illumina pair-end reads (Forward lib-24 million reads, Reverse Lib 24 million) using FASTX_Quality_Filter by applying the Q20 score to 90 percent of bases. (75 bp reads, insert size 200 bp)

But after filtering, I am observing around 18 million reads in a forward library and 20 million reads in a reverse library. I can see here 2 million bases difference between two libraries. Can I use above libraries for making transcriptome assembly purpose given that the number of reads are unequal?

Regards Rahul
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Old 03-01-2016, 12:17 PM   #2
mastal
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You will have problems with downstream analysis because the Forward reads and Reverse reads in your files will be out of sync, unless the reads where one of the pair has been filtered out are in separate 'unpaired_reads' files.

Last edited by mastal; 03-01-2016 at 12:22 PM.
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Old 03-01-2016, 01:40 PM   #3
GenoMax
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@Rahul: You should have used a paired-end aware trimming program to begin with.

At this stage you can use the repair.sh program from BBMap suite as follows:

Code:
$ repair.sh in1=r1.fq in2=r2.fq out1=fixed1.fq out2=fixed2.fq outsingle=singletons.fq
This will re-sync the order of your trimmed files and separate the single reads that remain into a separate file.
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fastx toolkit, quality assessment, rnaseq alignment, soapdenovo-trans

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