I am having some problens in work with GATK. The first thing is my sequences are paired-end and I nedd to pass in cutadapt to cut the parts that are not good, but the sequence_1 and sequence_2 stayed with differents sizes.
After that I just passed in bowtie2 to map and after I passed in samtools to transform in .sam, .bam and sort the sequences.
In the end, when I put GATK to run, they run the firste part: AddOrReplaceReadGroups, then give a error that saus that one or more argumments or inputs im my command are wrong. But I always use the same script to run java (if end-to-end and paired-end) and work.
The only thing I do this time that changes is that I use cutadapt and generated a different two input sizes (but I need to cut, because the sequences i am using are not good).
Someone knows something about that?
Thanks a lot