I’m trying to generate my own (very short) bed file, and I’d very much appreciate some input as to whether my thinking is sound. So:
When analyzing my RNA-Seq data with Tophat I’ve found some novel transcripts that I’d like to analyze further. For some of the downstream things I want to do, I need their coordinates in bed files. Tophat gives me coordinates for splice junctions, and when I download genomic sequence from UCSC I can confirm putative splice sites. Just as an example: my gene, which is on the minus strand, consists of two exons. Exon 1 starts at Chr2 position 200,000,500 and the last nucleotide included in the exon is at 200,000,400. Exon 2 starts at (the first nucleotide in the exon is) 200,000,100 and the last included nucleotide is at 200,000,050. Then how do I put this down in a bed file? This is my attempt:
First row:
Column 1 is easy: Chr2.
Column 2: My first row should be the end of my second exon, since my gene is on the minus strand. Bed format is 0 based, so everything has to be decreased by 1. The number entered should be the first included nucleotide. That means I should put 200,000,049?
Column 3: The beginning of exon 2. Again, 0-based format, so everything is decreased by 1. However, the nucleotide entered should be the first one not included in the sequence, so that means +1 again. Thus, I should enter 200,000,100.
Column 4: Score. I don’t have a score so I’m just putting a number
Column 5: Strand. I’m putting –
Second row:
Column 1: Chr2
Column 2: According to the same logic as above, end of exon 1: 200,000,399
Column 3: 200,000,500
Column 4: Made-up score
Column 5: -
Am I getting this right? Thank you!
When analyzing my RNA-Seq data with Tophat I’ve found some novel transcripts that I’d like to analyze further. For some of the downstream things I want to do, I need their coordinates in bed files. Tophat gives me coordinates for splice junctions, and when I download genomic sequence from UCSC I can confirm putative splice sites. Just as an example: my gene, which is on the minus strand, consists of two exons. Exon 1 starts at Chr2 position 200,000,500 and the last nucleotide included in the exon is at 200,000,400. Exon 2 starts at (the first nucleotide in the exon is) 200,000,100 and the last included nucleotide is at 200,000,050. Then how do I put this down in a bed file? This is my attempt:
First row:
Column 1 is easy: Chr2.
Column 2: My first row should be the end of my second exon, since my gene is on the minus strand. Bed format is 0 based, so everything has to be decreased by 1. The number entered should be the first included nucleotide. That means I should put 200,000,049?
Column 3: The beginning of exon 2. Again, 0-based format, so everything is decreased by 1. However, the nucleotide entered should be the first one not included in the sequence, so that means +1 again. Thus, I should enter 200,000,100.
Column 4: Score. I don’t have a score so I’m just putting a number
Column 5: Strand. I’m putting –
Second row:
Column 1: Chr2
Column 2: According to the same logic as above, end of exon 1: 200,000,399
Column 3: 200,000,500
Column 4: Made-up score
Column 5: -
Am I getting this right? Thank you!
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