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Old 10-29-2019, 09:06 AM   #3
Location: Brazil

Join Date: Aug 2015
Posts: 92

Hi! Yes you can BLAST it, but since it's a short sequence it's best if you use the `blastn` algorithm instead of the `megablast` one. You can also decrease the word size to 7 to increase sensitivity.

Here's your search, it'll be available until october 31:

According to the BLAST results, the sequence matches chr2:29446798-29446833 (hg19).

...PS anyways the CIGAR string says "36M" but the alignment to GRCh37.p13 shows one mismatch.

...PPS oh, I just noticed - I know where you got it wrong! Bit 16 in the SAM flag does not simply mean "the read is aligned to the reverse strand", it means "the read is represented as its reverse-complement because it aligned to the reverse strand". Sequences in SAM files are always represented on the forward strand. So if bit 16 is 1, as in this case, it means that "CCCC..." is ALREADY the reverse-complement of the actual read. So you don't have to reverse-complement it again. In fact, you can find your sequence in the same screenshot you posted.

Last edited by r.rosati; 10-29-2019 at 09:46 AM.
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