Hello everyone,
I am new in the field of bioinformatics and I am currently looking for a good alignment viewer. I have run several alignments using blast and blat software and would like to view the resulting alignments (RNA-seq).
I made some researches and found several viewers including SAMtools, MapView, MAQ viewer, GAP5, Consed or even the ShortRead package from Bioconductor, but none of them seems to be able to read output from Blast of Blat (.psl).
Since SAMtools can handle gapped alignments, I tried to use the third party convertors that come with it (such as psl2sam) but it does not seem to work correctly. The only official convertor that comes with SAMtools takes MAQ files as input, which I do not have. Other viewers such as MapView or GAP5 also rely on other input formats such as MAQ or ELAND.
So my question is simple. Do you know if there are viewers that can handle blast and blat alignments directly or indirectly (using approved converters), or do you think it would be faster to develop my own viewer to handle this particular problem of input format ?
Thanks
I am new in the field of bioinformatics and I am currently looking for a good alignment viewer. I have run several alignments using blast and blat software and would like to view the resulting alignments (RNA-seq).
I made some researches and found several viewers including SAMtools, MapView, MAQ viewer, GAP5, Consed or even the ShortRead package from Bioconductor, but none of them seems to be able to read output from Blast of Blat (.psl).
Since SAMtools can handle gapped alignments, I tried to use the third party convertors that come with it (such as psl2sam) but it does not seem to work correctly. The only official convertor that comes with SAMtools takes MAQ files as input, which I do not have. Other viewers such as MapView or GAP5 also rely on other input formats such as MAQ or ELAND.
So my question is simple. Do you know if there are viewers that can handle blast and blat alignments directly or indirectly (using approved converters), or do you think it would be faster to develop my own viewer to handle this particular problem of input format ?
Thanks
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