I have 2 questions.
- I am working on RNA-seq data and using Hisat. I am submitting it as job. my script is
hisat2 -p 55 -x <htidex files> -q (to recognize fastq) -1 <file1_pairedend> -2 <file2_pairedend> -S /path/xyz.sam &> /path/xyz.sam.info(I worked with the same command but never had problem) I am getting sam files but my sam.info file has 0 kb.
- Also, after using SAMTOOLcommand:
samtools view -bS test.sam > test.bamI am getting error message "SAM header is present: 194 sequences. Parse error at line 39349126: missing colon in auxiliary data Aborted". What could be the cause for both the issues.Can somebody help please. Thanks