I noticed that hisat2_read_statistics.py treats input files as FASTA by default, even when I specify the -q option (intended for FASTQ files). Thus, FASTQ files not suffixed with .fastq or .fq are recognized as FASTA, resulting in obviously incorrect and random read length calculations. The alignment process sometimes still proceeds without reported errors. So I wonder: can these alignment results be trusted, and how much does the --read-lengths parameter actually matter?
Case1 ：Error reported with :--read-lengths arg must be at least 20;
Case2： normal information
In both case, command
"hisat2 --dta-cufflinks -p 64 -q -x ~/Reference/**_index -1 ../fastp/$file_1.fp.gz -2 ../fastp/$file_2.fp.gz | samtools view -bS -q 20 - > $name.bam " were used.
I noticed that hisat2_read_statistics.py treats input files as FASTA by default, even when I specify the -q option (intended for FASTQ files). Thus, FASTQ files not suffixed with .fastq or .fq are recognized as FASTA, resulting in obviously incorrect and random read length calculations. The alignment process sometimes still proceeds without reported errors. So I wonder: can these alignment results be trusted, and how much does the --read-lengths parameter actually matter?
Case1 ：Error reported with :--read-lengths arg must be at least 20;
Case2： normal information
In both case, command
"hisat2 --dta-cufflinks -p 64 -q -x ~/Reference/**_index -1 ../fastp/$file_1.fp.gz -2 ../fastp/$file_2.fp.gz | samtools view -bS -q 20 - > $name.bam " were used.