BLAST geneate Output SAM file , Missing aligned sequences.

Question

[clear.choi]

I have tried to use ncbi blast 2.3.0 version which support output sam file.

I did it like below,

/program/ncbi-blast-2.3.0+/bin/blastn -db /db/class2.db -max_target_seqs 1 -outfmt 17 -query ./S4--S4.fasta -out ./S4--S4.sam

Then I got strange results that first all reference Name and Query Name is wrongly generated.

For example.expected name

queryname = m160213_235908_42273_c100966372550000001823205304301641_s1_p0/32769/0_2213 0.89 28
Reference name = HLA_HLA00688_DRB1_04_03_01_15246_bp

real name,

Query name = BL_ORD_ID:16
Reference Name : Query_1

And also there is no sequences are generated only Cigar , position, Map Quality, I want to put sequences also,

Do you have any idea how to handle blast with output as SAM file?

[SES]

There is the blast2sam.pl script from samtools. IIRC, this requires the standard pairwise format, which is the least stable, so it may or may not work with the latest blast version.

Answer 1

[Pierre Lindenbaum]

SAM in blast 2.3.0 is still beta

FYI: my student wrote a blast2sam tool