I'm having trouble obtaining the exact chromosome number, when using standalone BLAST. My current setting is like below:
/...BLAST/blast-2.2.29+/bin/blastn -db GPIPE/9606/105/GCF_000001405.25_top_level -query test.fasta -out test.out -task blastn -outfmt 6 -remote -word_size=15
,where the database is GRCh37.
The result looks like:
sample1 gi|441431411|ref|NW_004166863.1| 100.00 41 0 0 38 78 527422 527382 1e-012 77.0
As you can see, there is gene id and the position of the reference sequence, but there is no chromosome number. I couldn't find this option in the format specifiers blast provided either. I know I could get what I want by standalone BLAT, but I need to ensure BLAST also works, because it has a windows version. I also understand if I use a XML or query-anchored format, I could locate the chromosome information in a hard way. However I'm just disappointed that I can't find it in the tabular format... Could some help me please?