How I know a file is sam or bam, sorted or unsorted

Question

[zizigolu]

Hi

I have a file by STAR alignment, I supposed to get a bam file but I obtained Aligned.out.sam

Is there any command to check if this file is a .bam or .sam file? A command to check this file sorted or unsorted?

Thank you so much

Answer 1

[Arup Ghosh]

Check the error log if STAR had any memory issues, --outSAMtype BAM SortedByCoordinate is supposed to sort the output.

[Friederike]

Just to follow up on Arup's advice -- given that you seem to have generated a SAM file instead of a BAM file, it seems highly likely that the conversion and sorting failed [EDIT:], therefore it would be highly advisable to understand what caused STAR to not honor your parameter choices, i.e. read the log file(s) and see if you can pinpoint the error that must have occurred.

[zizigolu]

This command gave sorted bam using STAR

STAR --runThreadN 4 --genomeDir ./STAR_hg38_Genome --readFilesIn 1.fastq 2.fastq --limitBAMsortRAM 64606632121 --outFileNamePrefix ./SeqBatch2/ --outSAMtype BAM   SortedByCoordinate --outSAMmode Full --outSAMstrandField intronMotif

[Friederike]

So it was a problem with the memory. It'd be great if you could accept the answer that suggested that so that other users in the future will be pointed to the right track immediately.

Answer 2

[Arup Ghosh]

Check the bam/sam file header line using samtools samtools view -H Aligned.out.sam |grep "@HD" if you see SO:coordinate is present, it means the output is sorted. For STAR sorted/unsorted output check the STAR aligner manual section 4.3 .

[zizigolu]

This is the results

[fi1d18@cyan01 ~]$ samtools view -H Aligned.out.sam |grep "@HD"
@HD     VN:1.4
[fi1d18@cyan01 ~]$

Unsorted?

[Arup Ghosh]

Yes the output is unsorted.

[zizigolu]

That means this STAR command does not work

STAR --genomeDir ./STAR_hg38_Genome --readFilesIn ./1.fastq ./2.fastq --outSAMtype BAM SortedByCoordinate

Because I expected by adding --outSAMtype BAM SortedByCoordinate to STAR alignment I am getting a sorted .bam as output

[27atcggcta27]

you could try to output both and see if there is a difference,

--outSAMtype BAM Unsorted SortedByCoordinate

check both files to see if either is sorted