Are you using the latest version of samtools and HTSlib? If not, please specify.
I am using the latest samtools 1.21
Please describe your environment.
- Linux 6.8.0-48-generic Ubuntu 22.04 LTS
- x86_64 architecture
- gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
- Ubuntu clang version 14.0.0-1ubuntu1.1
Please specify the steps taken to generate the issue, the command you are running and the relevant output.
I meet up with a problem with samtools fasta/fastq
I am trying to convert a bam file into fasta/fastq and the bam was generated by bowtie2 from pair-end 250 data.
50-F.zip
I used stats to get the info about reads and:
raw total sequences: 1856 # excluding supplementary and secondary reads
filtered sequences: 0
sequences: 1856
is sorted: 1
1st fragments: 928
last fragments: 928
reads mapped: 696
reads mapped and paired: 534 # paired-end technology bit set + both mates mapped
reads unmapped: 1160
reads properly paired: 0 # proper-pair bit set
reads paired: 1856 # paired-end technology bit set
and flagstat
1856 + 0 in total (QC-passed reads + QC-failed reads)
1856 + 0 primary
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
696 + 0 mapped (37.50% : N/A)
696 + 0 primary mapped (37.50% : N/A)
1856 + 0 paired in sequencing
928 + 0 read1
928 + 0 read2
0 + 0 properly paired (0.00% : N/A)
534 + 0 with itself and mate mapped
162 + 0 singletons (8.73% : N/A)
534 + 0 with mate mapped to a different chr
470 + 0 with mate mapped to a different chr (mapQ>=5)
but when I tried to get fasta/fastq file of the bam by
samtools fasta -1 50-F.fasta -2 50-R.fasta -s 50-single.fasta 50-F.bam
all reads output to single file. It is confused that 50-F.fasta and 50-R.fasta are empty.
And when -s (single) is not set, reads appears in 50-F.fasta and 50-R.fasta.
I also tried sorted and sorted by name bam file but the same.
Are you using the latest version of samtools and HTSlib? If not, please specify.
I am using the latest samtools 1.21
Please describe your environment.
Please specify the steps taken to generate the issue, the command you are running and the relevant output.
I meet up with a problem with samtools fasta/fastq
I am trying to convert a bam file into fasta/fastq and the bam was generated by bowtie2 from pair-end 250 data.
50-F.zip
I used stats to get the info about reads and:
and flagstat
but when I tried to get fasta/fastq file of the bam by
all reads output to single file. It is confused that 50-F.fasta and 50-R.fasta are empty.
And when -s (single) is not set, reads appears in 50-F.fasta and 50-R.fasta.
I also tried sorted and sorted by name bam file but the same.