Problems with dedup output and RSEM

Hi,

I’m using umi_tools dedup to remove PCR duplicates from an alignment to the transcriptome with STAR. After the deduplication, when I run RSEM, it seems that there are some reads from the pairs that are lost since the program exits with the following error: Read ST-E00114:1178:HFL75CCX2:7:1101:1610:55297_TTGCCATCTC: The adjacent two lines do not represent the two mates of a paired-end read! (RSEM assumes the two mates of a paired-end read should be adjacent)

The ran the command with --paired --multimapping-detection-method=NH --unpaired-reads=discard --chimeric-pairs=discard --unmapped_reads=discard

I have seen that this problem was already discussed in #384, but there is not an option on how to solve this. Do you have any idea on how to solve this issue or a workaround that could work for this case?

Thank you very much

[IanSudbery]

As for release schedule: I can’t see any reason not to include this script in the next release. We have a set of things we’d like to tidy up before the next release, but its probably not a million miles off.

[IanSudbery]

Yeah, I thought that it might be coming from $options.args. There is still a potential theoretical problem with situations where read1 is alignmed but read2 isn’t, so I’ll see what I can think of for that.