Warning: Detected 3573628 lines containing read pairs whose two mates have different names in RSEM?
Hi dear one,
I get this warning while running RSEM!
Warning: Detected 3573628 lines containing read pairs whose two mates have different names.
What should I do?
I am new to sequence analysis, please help me! Thanks in advance !
p.s. I use RSEM-1.3.0 and Bowtie 2 version 2.2.6 !
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It seems your fastq files are unpaired. Did you pre-proccess them (trim adapter, bad quality, etc)? Tell us the command lines used for any pre-proccessing, and for performing the alignment.
If you are new, read this:How To Ask Good Questions On Technical And Scientific Forums
Fastq-dump is maybe adding .1 and .2 to your reads name, what options did you use for this program? Check that the name of your read mates is the same in the two files (eg first line of file_1 should be exactly the same of the first line of file_2).
yes thank you for your valuable comment