BLAST geneate Output SAM file , Missing aligned sequences.
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?
• 5,003 views
•
link
updated
by
Ram
•
written
by
clear.choi •
•
written
by
clear.choi •
1 answer
SAM in blast 2.3.0 is still beta
FYI: my student wrote a blast2sam tool
• 0 views
•
link
updated
by
Ram
•
written
by
Pierre Lindenbaum
•
written
by
Pierre Lindenbaum
Log in to answer this question.
More posts like this
-
How can I solve the database error?
written by Kenan.gk •
-
Running blastn to get best hits match using (-max_target_seqs 1 -max_hsps 1 ) ?
written by sunnykevin97
-
Puzzling NCBI BLAST+ output after transcriptome assembly
written by ella •
-
tBlastn taking an absurd amount of time
written by Rogerio Ribeiro •
-
local blastx output
written by agata88
-
blast error: Syntax error in system-wide configuration file: NCBI C++ Exception
written by lidanqing1990 •
-
Modifying Standalone BLAST output
written by glady
-
BLAST Search to get original sequences or find fully amplified segment.
written by clear.choi •
-
NCBI Blast Results parser [Use only score info]
written by clear.choi •
-
NCBI Blast Search Program Alignment Issue.
written by clear.choi •
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.