Hi All Im new on here. i was after advice concerning the 100bp PE reads:
Q1) I have heard it is a problem bioinformaticaly that if you do 100bp PE reads, you ideally don't want the reads from either end to overlap (ie more than 100bp+ from either end) coz if they do you can't align these easily.
Q2) Following on from Q1 the reason I ask this is that I would like to sequence directly from 200bp PCR fragments as I am hoping to index 96 samples in a single lane. So is it possible to sequence many (~150) amplicons that are all 200bp long, I guess adapters and barcodes would be added to these after PCR.
so ~150 x 200bp amplicons for 96 patients using 100bp PE reads, therefore achieving 200bp reads that would hold allele specific information for that one paired end read. Also I really have no other option but to use PCR products - but to maintain the read along the full length.
Can anyone help
Q1) I have heard it is a problem bioinformaticaly that if you do 100bp PE reads, you ideally don't want the reads from either end to overlap (ie more than 100bp+ from either end) coz if they do you can't align these easily.
Q2) Following on from Q1 the reason I ask this is that I would like to sequence directly from 200bp PCR fragments as I am hoping to index 96 samples in a single lane. So is it possible to sequence many (~150) amplicons that are all 200bp long, I guess adapters and barcodes would be added to these after PCR.
so ~150 x 200bp amplicons for 96 patients using 100bp PE reads, therefore achieving 200bp reads that would hold allele specific information for that one paired end read. Also I really have no other option but to use PCR products - but to maintain the read along the full length.
Can anyone help
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