Hi everyone,

After quite a bit of searching the threads on this forum, I'm still not exactly sure how TopHat deals with an input fastq file that contains reads of different lengths (e.g. 51bp and 76bp). I assume that equal read lengths throughout the file would be ideal, but I have four 76bp lanes and one 51bp lane from the same library and would like to use all the data if possible. Any advice from the TopHat/Bowtie power users out there?

Thanks in advance,

Shurjo

After quite a bit of searching the threads on this forum, I'm still not exactly sure how TopHat deals with an input fastq file that contains reads of different lengths (e.g. 51bp and 76bp). I assume that equal read lengths throughout the file would be ideal, but I have four 76bp lanes and one 51bp lane from the same library and would like to use all the data if possible. Any advice from the TopHat/Bowtie power users out there?

Thanks in advance,

Shurjo

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