Web Page Converting Seq Mapping Score

Question

[kanwarjag]

I am sure it is a very simple question and has been answered here, however I could not find it and has googled it too. I used to use a web page where you add the mapping score after BWA/ Bowtie 2 alignments like 16, 274 -----. it will tell me whether reads are uniquely aligned, one mate aligned aligned to reverse strand and so on. However I am not finding that page Could some one point me to that URL I have spent lot of time searching this. I promise to book mark the site.

Thanks

Answer 1

[Chris Miller]

I think you're talking about SAM flags and referring to this very useful webpage: http://picard.sourceforge.net/explain-flags.html

Answer 2

[Simply Bioinformatics]

Four Main reference Site that You might need during your adventure:

ENJOY ;)

1) https://broadinstitute.github.io/picard/explain-flags.html

2)http://www.samformat.info/sam-format-flag

3)http://www.samformat.info/sam-format-flag-single

4)https://ppotato.wordpress.com/2010/08/25/samtool-bitwise-flag-paired-reads/