Megablast ***** No hits found ******

[NGSnoob]

Hi,

I am doing Megablast job with a high Wordsize (45) for short reads 50 bp.
Is it possible to turn off the reads with ***** No hits found ****** for the outputfile, because most of my reads (ca. 95%) have no hits.

[sklages]

maybe you should use a different output format, like -D 3. That's what I usually use for screening purposes.

Sven

[malachig]

Perhaps the reason you have so many reads without hits is a combination of random errors in your reads and the word length you have chosen. A word length of 45 for 50-mer reads virtually guarantees that only perfect matches will be found ... One of the advantages of BLAST compared to some next gen. sequencing aligners is the potential to detect arbitrary numbers of mismatches and/or gaps. But that only works if the parameters are chosen accordingly. Word size in particular needs to be small. For a read size of 50 I would chose a word length of ~15 so that even if a read has 3 mismatches evenly distributed across the read, you can still find the alignment.