Question: Are these steps correct? Galaxy
gravatar for rus2dil
4.2 years ago by
Sri Lanka
rus2dil20 wrote:

I have aligned NGS six runs of a sample using BWA (galaxy platform). Then I merged them into one BAM file. Next I sliced the region of interest using SliceBAM in BED tools. After that I merged sequences in the resulting file using Merge command in Operate on Genomic Intervals. So the final result is a BED file. How can I convert this BED file into a FASTA file?

ADD COMMENTlink modified 4.2 years ago by marina.v.yurieva480 • written 4.2 years ago by rus2dil20
gravatar for marina.v.yurieva
4.2 years ago by
Farmington, CT
marina.v.yurieva480 wrote:

I don't think you can do it in Galaxy but you can convert with bedtools getfasta

ADD COMMENTlink written 4.2 years ago by marina.v.yurieva480
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