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Old 08-26-2015, 09:29 PM   #1
arkilis
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Default Does anyone use PEAR before

I am trying to merge two illumina reads set, R1 and R2. However R1 has one particular read named read1 which can NOT be found in R2.

The file after merging only contains part of read1. So how to use PEAR to do a merge which include all the sequence of read1 in the merged file?

Thanks,
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Old 08-27-2015, 06:11 AM   #2
azneto
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I like to use flash2 to do it (https://github.com/dstreett/FLASH2).
These software assume both files contain the exact same number of reads.
You should manage to get rid of unpaired reads.
Please find attached a script that can solve that.
-Cheers
Attached Files
File Type: pl mergeShuffledFastqSeqs.pl (4.5 KB, 4 views)
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Old 08-27-2015, 10:29 PM   #3
arkilis
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Wink

Quote:
Originally Posted by azneto View Post
I like to use flash2 to do it (https://github.com/dstreett/FLASH2).
These software assume both files contain the exact same number of reads.
You should manage to get rid of unpaired reads.
Please find attached a script that can solve that.
-Cheers

Thanks. Looks like flash2 do the similar job of PEAR.
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Old 08-28-2015, 02:58 AM   #4
GenoMax
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There are many programs that can do read merging. BBMerge.sh from BBMap is also user friendly.
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