I did ChIPseq analyses a couple of times and it always worked quite nicely.
So, now I have the problem that I have fastq files (size 700-1000MB) which I can trim at first without any problems, but after bowtie2 the error message below occurs and my file is below 1KB?!
Error: Read Error: Read SRR619423.17 1_13_196/1 has more quality values than read characters.
Error: Read SRR619423.81 1_22_371/1 has more quality values than read characters.
Error: Read SRR619423.65 1_19_1131/1 has more quality values than read characters.
Can somebody help me what I am doing wrong or what I do have to change to make it work?
Thank you in advance for your help!