I am doing RNA-seq analysis using usegalaxy.com and this is my first time to do that. I have a problem in the bed file, UCSC genome browser does not recognize the file, as it does not contain ''chr1'' in the QNAME column. The BED file that I`ve created as the following: (The format of the gene reference is FASTA )
QNAME FLAG RNAME POS MAPQ CIGAR AL939114.1 0 139 J00125:34:HTJT7BBXX:5:1101:16670:2703/2 8 +
How can I change the content of QNAME to chr1 and How can I insert start and end in the position column instead of '' J00125:34:HTJT7BBXX:5:1101:16670:2703/2'' ??.