tophat 2.0.10:WARNING: read pairing issues detected (check prep_reads.log) !

[kesner]

I am aligning paired end reads that have been trimmed of adapters with cutadap using tophat 2.0.10.

Paired read log has this:
/PHShome/bak22/src/tophat-2.0.10.Linux_x86_64/prep_reads: /lib64/libz.so.1: no version information available (required by /PHShome/bak22/src/tophat-2.0.10.Linux_x86_64/prep_reads)
prep_reads v2.0.9 (3067M)
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WARNING: read pairing issues detected (check prep_reads.log) !
Pair #400691 name mismatch: D64TDFP1:1:1103:2790:5963#0/1 vs D64TDFP1:1:1103:2792:5883#0/2
11670 out of 41376603 reads have been filtered out
149176 out of 41376603 read mates have been filtered out
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I check both records and they are fine. However the entry prior to each, although matching 1 of the paried ends is a totally trimmed records. That is both prior to and after the '+'. They have nothing.
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I am wondering if this warning is a caused by a problem in tophat which can't handle such reads.

Has anyone else seen this? Is it a serious problem?

[dpryan]

Just use a wrapper for cutadapt, like trim_galore, that can filter out orphaned mates and prevent the read pairing issue.

[kesner]

thanks I'll try it

[ronaldrcutler]

I ran into the same problem while trying to multithread. I found that not multithreading seemed to fix it but was then running into it again even when not using multithreading.

I am using a script to have tophat2 go through a folder with read pairs and align those and automatically move on to the next. However, I saw that it would start to randomly use different mate pairs from different lanes instead of the same one from the same lane.

In order to fix this I just made a new folder and copied the reads and now everything seems to work okay, and with multithreading!