Error: failed to retrieve right read for pair # 243418 !

Question

[baurumon]

Hi ,

I am using tophat2 for alignment which is showing "Error: failed to retrieve right read for pair # 243418 !". Then i used BBTools to repair seq data with - "repair.sh in1=broken1.fq in2=broken2 out1=fixed1.fq out2=fixed2.fq outs=singletons.fq repair" but still getting same issue.

How can i solve this issue?

Thanks in advance!!

[GenoMax]

Can you show us examples of reads from the R1/R2 files? Perhaps your read headers may be corrupt.

[baurumon]

[GenoMax]

It looks like the submitters in this case did not preserve original Illumina format headers so you are not going to be able to recover them.

You will need to use reformat.sh from BBMap suite with one of the following options to force them into an Illumina header format.

addslash=f              Append ' /1' and ' /2' to read names, if not already present.  Please include the flag 'int=t' if the reads are interleaved.
addcolon=f              Append ' 1:' and ' 2:' to read names, if not already present.  Please include the flag 'int=t' if the reads are interleaved.

[baurumon]

Hi, I used reformat.sh from BBmap with this command: "reformat.sh in1=pair1.fq in2=pair2.fq out1=renamed1.fq out2=renamed2.fq addslash=f int=t " and run again in tophat2 .But unfortunately got the same Error again.

Is there some other way to solve it?

Thanks in advance Rabbani

[Benn]

Check if header of pair # 243418 are correct

[nedoluzhko]

So, I have the same problem. The noob question: How can I check it and even delete this pair from the dataset?