read different length in fastq

[m_elena_bioinfo]

Dear,
I have performed two runs (targeted sequencing) on miseq using 2x150bp protocol. Unusually, I have obtained fastq containing reads of different length, that during alignment step cause misalignment errors (and a lot of false positives). Any idea for the reason? Any idea to fix it?

[Apexy]

Hello,
I do not think read length is the problem except the reads incorporate many uncalled and wrong bases. Did you perform read thinning or trimming ? By false positive, do you mean that the reads align elsewhere than expected ordo you mean the reads do not have a hit? What is he range of read lengths? What alignment tool are you using? What are you aligning the reads to.

[mastal]

read different lengths in fastq

Hi elena,

My experience with Illumina sequencing is that all the reads should be the same length.

Have the reads been trimmed to remove low quality regions or adaptor sequences?

Best wishes,
Maria