Hey, I need to download BAM files of breast cancer cell lines from GEO/SRA. For example I will use SRR925780.
I tried to do it in 2 ways:
SRA run browser: http://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR925780. Where I need to download a separate file for each chromosome but the download is very fast (4 Gb in about 10 minutes) and the output file is a BAM file which means no other tool is needed.
SRA toolkit, following their manual, I run this command:
sam-dump SRR925780 | samtools view -bS - > SRR925780.bam
It takes about 3 hours to download and convert 100 Mb! The time diff is too big, I am wondering what am I doing wrong with the SRA toolkit ans samtools.
BTW I work with the latest SRA toolkit but the samtools version is old, it's the only one I found working for Windows: https://bow.codeplex.com/releases
So my questions are:
- Could it be the fastest way to download BAM files is manually via SRA run browser ?
- Is there a way to run a newer version of samtools on Windows?