I blasted locally a series of short dna queries - all in one fasta file - against portions of ngs reads from the same set: 10 reads, then 100, 1000 and finally 10k reads. Each read portion included all the smaller ones. But the number of hits that the blast report contained seems to be reaching a plateau rather than increase more or less proportionally. I also noticed that that the reads with hits for a given query don't accumulate as the number of reads blasted increases: reads with hits found when blasting 1000 reads are generally different from those found when blasting against 10k reads instead of the former always being included in the latter. Max_hsps option doesn't have any effect, max_alignments doesn't change much either. In contrast, blat seems to behave the 'correct' way. Is blast adjusting some parameters to increase speed as the size of dna database increases? If I understand it correctly, there's a comp_based_stats option for protein alignment (blastp) to control just that but not for blastn which I'm using. How can I make blastn report all the alignments that fit the criteria with no adjustments for dna db size? Must be something simple I'm missing here...
Question: blastn report apparently not showing all of the alignments, probably re-adjusting parameters, which option can control that?
21 months ago by
prishly • 10
prishly • 10 wrote:
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