Hi,
I need to analyze publicly available gro-seq data. But I am new to these kind of analysis.
1) It is written in the GEO
"Bed files are tab-separated text files in which columns represent: chrom, chromStart (5' End of the read), chromEnd (chromStart+1), name (unused always 'n'), score (the number of mismatches), and strand. "
I need to find tags near TSS of genes. For genes on the minus strand what should be my approach?
2) I am using refseq annotation files from USCD. For example for gene BLNK (NM_001114094) which is on negative strand, txstart (97941444) and txend (98021323)
From below post
"Genomic coordinates that we store and display are always relative to the
positive strand of the reference genome. We reverse-complement genomic
sequence when a gene is on the reverse strand, but genomic coordinates
are still forward. So for a gene on the reverse strand, txStart is its
3' end, txEnd is its 5' end, and the exon coordinates are listed 3' to
5' (backwards)."
Therefore I am treating txend (98021323) is txstart and txstart (97941444) as txend.
3) When I try to find corresponding gro-seq tags what should be my approach for negative strand
For example a chr is 1000 bp. a gene in negative strand according to ucsd convention id from 10(txend) to 100(txstart).
According to gro-seq files since it is starting from 5' coordinates that I should look
a) 10 (txend) - 100 (txstart)
b) 900(txend) - 990(txstart)
I am a bit confused. Can anyone help me?
I need to analyze publicly available gro-seq data. But I am new to these kind of analysis.
1) It is written in the GEO
"Bed files are tab-separated text files in which columns represent: chrom, chromStart (5' End of the read), chromEnd (chromStart+1), name (unused always 'n'), score (the number of mismatches), and strand. "
I need to find tags near TSS of genes. For genes on the minus strand what should be my approach?
2) I am using refseq annotation files from USCD. For example for gene BLNK (NM_001114094) which is on negative strand, txstart (97941444) and txend (98021323)
From below post
"Genomic coordinates that we store and display are always relative to the
positive strand of the reference genome. We reverse-complement genomic
sequence when a gene is on the reverse strand, but genomic coordinates
are still forward. So for a gene on the reverse strand, txStart is its
3' end, txEnd is its 5' end, and the exon coordinates are listed 3' to
5' (backwards)."
Therefore I am treating txend (98021323) is txstart and txstart (97941444) as txend.
3) When I try to find corresponding gro-seq tags what should be my approach for negative strand
For example a chr is 1000 bp. a gene in negative strand according to ucsd convention id from 10(txend) to 100(txstart).
According to gro-seq files since it is starting from 5' coordinates that I should look
a) 10 (txend) - 100 (txstart)
b) 900(txend) - 990(txstart)
I am a bit confused. Can anyone help me?