problem with piping samtools sort

Question

[pr.khavari]

Hi everyone, I wanna prepare my alignment bam file for cufflinks running. I 've used samtools sort for converting sam to bam, next I gonna to run my script for sorting it, but it don't work. Do you have any recommendation or suggestion for correction of that? thanks so much for help me.

my scripts is here:

./samtools view -@ 4 /media/marziyeh/56F72A78084DABD5/RNA-seqdata/output_bowtie2_alignment_ref/sample33.sam > sample33.bam`

`

 ./samtools sort -n -l 9 -@ 4 -m 3G /media/marziyeh/56F72A78084DABD5/RNA-seqdata/viewed_samtools/sample32_sortedin22.bam >> /media/marziyeh/56F72A78084DABD5/RNA-seqdata/sorted.sample/sample.32

or another script as well as same result;

 cd /media/marziyeh/56F72A78084DABD5/RNA-seqdata/viewed_samtools/;/home/marziyeh/Software/samtools-1.6/samtools sort -n -l 9 -@ 4 -m 3G -o /media/marziyeh/56F72A78084DABD5/RNA-seqdata/sorted.sample/sample32_sorted.bam -O bam -n -T /media/marziyeh/56F72A78084DABD5/RNA-seqdata/sorted_file -@ 4 /media/marziyeh/56F72A78084DABD5/RNA-seqdata/viewed_samtools/sample32_sortedin22.bam

Error is here: [E::sam_parse1] missing SAM header [W::sam_read1] Parse error at line 1 samtools sort: truncated file. Aborting

Answer 1

[Samarth Kulshrestha]

Yor error message hints that your generated output BAM is without header section. Please check for header section using command below

samtools view -H yourfile.bam

Above command should print Header only (No alignment section)

[pr.khavari]

thanks, I'm run your suggestion now with this command line; ./samtools view -H /media/marziyeh/56F72A78084DABD5/RNA-seqdata/viewed_samtools/sample32_sortedin22.bam but gives anything.

[Samarth Kulshrestha]

To include header section to your output BAM run samtools command:

• samtools -bhS yourfile.sam > yourfile.bam

Here parameter indicates that

• b: your output will be in BAM format
• h: print header for the SAM output
• S: input is SAM

After performing this step, sort yourfile.bam using samtools sort command

Hope this works Best