Hi all,

I downloaded from NCBI a .sra file relative to a chip-Seq experiment (GEO: GSE19235).

I converted the .sra file into a .fastq file using fastq-dump. Afterwards, I tried to map the reads onto hg19 genome (tried with hg18 as well but the result did not change) using bwa-mem. The .sam file was converted to a .bam file using samtools, in order to eventually create a .bed file.

Problem: the .bam file is not empty, but no reads have been succesfully mapped onto the genome (any), as the output from samtools flagstat suggests:

samtools flagstat 263A-SRR030756_sorted.bam

8776181 + 0 in total (QC-passed reads + QC-failed reads)

0 + 0 secondary

0 + 0 supplementary

0 + 0 duplicates

0 + 0 mapped (0.00%:-nan%)

0 + 0 paired in sequencing

0 + 0 read1

0 + 0 read2

0 + 0 properly paired (-nan%:-nan%)

0 + 0 with itself and mate mapped

0 + 0 singletons (-nan%:-nan%)

0 + 0 with mate mapped to a different chr

0 + 0 with mate mapped to a different chr (mapQ>=5)

Can anyone help me to understand what is going on?

Any other mapper around to try? and how different may they be?

Thanks in advance,

Daniele