I'm wondering if someone out there would please answer a question for me about SAM files and ways to interact with their underlying alignment data.
I used bowtie2 to make alignments between two short test sequences in fasta format, using GRCh38 as an index file (details pasted below). The SAM file with info detailing the alignment is in the SAM file, of course -- but the general question I have is, how, if at all, can I render this alignment data in the style of a more traditional view like a BLAST alignment? What tool can read the SAM content and render an alignment in text format that looks something like the BLAST alignments pasted below?
Thank you.
Example blastn alignment result:
(identity 'ticks' are not properly aligned in this cut&paste text example, but the concept is there)
>NC_000010.11 Homo sapiens chromosome 10, GRCh38.p12 Primary Assembly
Length=133797422
Score = 250 bits (151), Expect = 2e-64
Identities = 151/151 (100%), Gaps = 0/151 (0%)
Strand=Plus/Plus
Query 1 ATGCCCTACATATCACACCCCCAGTAATATCTTTCTGATAAGCAGACTTATCAACACTTC 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 90921451 ATGCCCTACATATCACACCCCCAGTAATATCTTTCTGATAAGCAGACTTATCAACACTTC 90921510
Query 61 ACTTAGGGGAAACTTGTCCCAGGACATCCTATTCCCTGGGTAAACAGCCTGAGGGGAAGG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 90921511 ACTTAGGGGAAACTTGTCCCAGGACATCCTATTCCCTGGGTAAACAGCCTGAGGGGAAGG 90921570
Query 121 GATCTGGGCCCTAAAGGCACTTGTCTATATC 151
|||||||||||||||||||||||||||||||
Sbjct 90921571 GATCTGGGCCCTAAAGGCACTTGTCTATATC 90921601
>NC_000010.11 Homo sapiens chromosome 10, GRCh38.p12 Primary Assembly
Length=133797422
Score = 182 bits (110), Expect = 3e-44
Identities = 131/151 (87%), Gaps = 20/151 (13%)
Strand=Plus/Plus
Query 1 ATGCCCTACATATCACACCCCCAGTAATATCTTTCTGATAAGCAGACTT----------- 49
|||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 90921451 ATGCCCTACATATCACACCCCCAGTAATATCTTTCTGATAAGCAGACTTATCAACACTTC 90921510
Query 50 ---------AAACTTGTCCCAGGACATCCTATTCCCTGGGTAAACAGCCTGAGGGGAAGG 100
|||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 90921511 ACTTAGGGGAAACTTGTCCCAGGACATCCTATTCCCTGGGTAAACAGCCTGAGGGGAAGG 90921570
Query 101 GATCTGGGCCCTAAAGGCACTTGTCTATATC 131
|||||||||||||||||||||||||||||||
Sbjct 90921571 GATCTGGGCCCTAAAGGCACTTGTCTATATC 90921601
example SAM content for these alignments below:
2 reads; of these:
2 (100.00%) were unpaired; of these:
0 (0.00%) aligned 0 times
2 (100.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
100.00% overall alignment rate
1] 0 NC_000010.11 90921451 42 151M * 0 0 ATGCCCTACATATCACACCCCCAGTAATATCTTTCTGATAAGCAGACTTATCAACACTTCACTTAGGGGAAACTTGTCCCAGGACATCCTATTCCCTGGGTAAACAGCCTGAGGGGAAGGGATCTGGGCCCTAAAGGCACTTGTCTATATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:151 YT:Z:UU
2] 0 NC_000010.11 90921451 0 49M20D82M * 0 0 ATGCCCTACATATCACACCCCCAGTAATATCTTTCTGATAAGCAGACTTAAACTTGTCCCAGGACATCCTATTCCCTGGGTAAACAGCCTGAGGGGAAGGGATCTGGGCCCTAAAGGCACTTGTCTATATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-65 XN:i:0 XM:i:0 XO:i:1 XG:i:20 NM:i:20 MD:Z:49^ATCAACACTTCACTTAGGGG82 YT:Z:UU
