SAMFormatException in aligned reads

[GiuliaGuiducci]

Hello all, I am analysing some ChIPseq data. I aligned the reads with Bowtie2 (using the pre-indexed human genome from Bowtie2 website, File: GRCh38 no-alt, analysis set), the command I used is the following.

bowtie2 -p 4 --no-unal -x pathwayto/GRCh38_noalt_as/GRCh38_noalt_as -1 ${forward_file_in} -2 ${reverse_file_in} -S ${Sample}.sam

The alignment report is good. The problem is that when I input the sam files in downstream processes (such as Sam Sorting (gatk) or Sam to Bam conversion (samtools) I get the following format error --> SAMFormatException: Error parsing text SAM file. length(QUAL) != length(SEQ), only on specific lines. I tried to remove specific lines but the error is found on downstream lines, so I am not sure it is the right way of troubleshooting.

Do you have any idea what could be the problem? I can repeat the alignment but I have no idea what to change in the script. Thanks in advance

Giulia

[ch4rr0]

Hello,

Would it be possible to provide the an example of the offending sequence in FASTQ format?

[ch4rr0]

Closing this issue due to lack of activity.