Re: [galaxy-user] Pre-processing of Illumina RNA-Seq paired end data

Hi Ravi, I got around this problem by using the fastq interlacer to join reads in to a single file, then use deinterlacer to output only reads that have a pair in the correct order. You may need to alter read IDs first by adding /1 and /2 to the end (see interlacer help text). I used

[galaxy-user] Pre-processing of Illumina RNA-Seq paired end data

Hello, I have Illumina 76bp paired end data for a zebrafish RNA-seq experiment and am basically stuck while trying to pre-process my data prior to using Tophat/CuffDiff. For each sample, I have a read1 fastq file and a paired read2 fastq file. After using FASTQ Groomer, I trimmed the ends

Re: [galaxy-user] Pre-processing of Illumina RNA-Seq paired end data

Hi, I think you need to first remove the adaptors and then trim the reads. That is probably the correct way. As for the second part of the question, you could try a rudimentary way to actually search for a sequence header. I have seen this different sizes in the r1 and r2 read files, but taken