0 + 0 mapped when used flagstat

Question

[chansik]

I've downloaded bam files from ENA, and tried samtools flagstat to confirm mapping.

But the result was like this. How do I interpret this?

Should I download fastq files?

Thanks

Answer 1

[GenoMax]

You may have downloaded unaligned BAM (uBAM) files. Yes there is such a thing where fastq files are converted to BAM without aligning them. You will need to convert the BAM files back to fastq and align them yourself.

[chansik]

Thank you, GenoMax!

I downloaded fastq files (read1 and read2) and ran fastQC but the quality doesn't seem any better. So I further deleted 15 bp of 5'end is it okay??

original fastq: https://www.dropbox.com/s/h1p4z51d3jk14et/ERR2593198_1_fastqc.html?dl=0 Trimmed (ngsShrot): https://www.dropbox.com/s/9cdcndrbawo91im/trimmed_ERR2593198_1_fastqc.html?dl=0 15bp trimmed: https://www.dropbox.com/s/pcqslx57jt4064a/15bp_trimmed_ERR2593198_1_fastqc.html?dl=0

Best regards,

[GenoMax]

This looks like this is an RNAseq experiment. There should be no need to delete 15 bp at 5'-end since it is because of this observation. You should either just trim to remove adapters or directly align to the genome/transcriptome.

You can add images to biostars posts using these directions.

[chansik]

Thank you again. I really appreciate your answer.

I just trimmed 15 bp at 5'end and this works pretty well in further processing