Timeline for Understanding the significance of BLAT score calculations for read fragment alignment
Current License: CC BY-SA 3.0
16 events
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| Dec 29, 2017 at 1:04 | history | edited | gringer♦ | CC BY-SA 3.0 |
remove aside, reformat BLAST, change question title to fit question, reorder question to give a better flow
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| May 20, 2017 at 12:45 | vote | accept | Sam Nicholls | ||
| May 18, 2017 at 15:44 | answer | added | Sam Nicholls | timeline score: 2 | |
| S May 18, 2017 at 14:38 | history | suggested | zx8754 |
new tags added/proposed
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| May 18, 2017 at 14:34 | review | Suggested edits | |||
| S May 18, 2017 at 14:38 | |||||
| May 18, 2017 at 12:11 | comment | added | Sam Nicholls |
@terdon Hah, no worries. A lot of bioinformatics is "damn, I need to run this with another tool". I'd happily move this to chat if you have any ideas. For what it's worth, BLAST is too slow (for the size of the data) and still doesn't give the granularity on gap information that I'm looking for :( Any thoughts?
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| May 18, 2017 at 12:09 | comment | added | terdon♦ | Fair enough (and sorry, didn't mean to appear pushy). I was just wondering if using another tool (like BLAST which would give you the e-values in a parseable table format) wouldn't be a simpler approach. I realize that "redo the analysis with this tool instead" is not a perfect solution though :). | |
| May 18, 2017 at 12:05 | comment | added | Sam Nicholls |
@terdon Thanks, I know what options BLAST has, but I'm asking about something else. I have updated my question to try and clarify though!
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| May 18, 2017 at 12:04 | history | edited | Sam Nicholls | CC BY-SA 3.0 |
added 2764 characters in body; edited title
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| May 18, 2017 at 11:17 | comment | added | terdon♦ |
BLAT might not, I admit I've only ever used BLAT online for simple things. BLAST, however (both NCBI and wublast), certainly does. Look at the "tabular" option for the -outfm flag in NCBI blast for example. I've spent more time than I care to remember parsing blast output, if you clarify the exact question you have, I should be able to help.
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| May 18, 2017 at 11:08 | comment | added | Sam Nicholls |
@terdon Despite my dislike of XML parsing, it seems a more structured way to get out the components of a hit compared to trying to infer structure from a sequence of lines. For what it's worth BLAT doesn't have flags for outputting an HSP per line.
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| May 18, 2017 at 10:49 | comment | added | terdon♦ | No! Not at all! The default output format for blast is a simple text file and there are flags to get one HSP per line (no sequence, only the scores etc). You can get XML as well but that's just a way of making your life harder IMO. Please edit your question and clarify what the original (scientific) question you are asking is. Are you looking for exact matches? Distant homologs? Finally, it would be better if you could include an example of your PSL file if that's really what you want parsed. | |
| May 18, 2017 at 10:05 | answer | added | holmrenser | timeline score: 1 | |
| May 18, 2017 at 9:37 | comment | added | Sam Nicholls | @holmrenser Don't you only get the HSPs by parsing the XML output? This is some laze on my part, as the HSPs in my XML described the hits from the perspective of the translated DNA, but I want to know where the alignments on the original sequence are without too much of my own error-prone interference. BLAT just gives the offset. It might be that I've overlooked something in the HSP data though... | |
| May 18, 2017 at 9:31 | comment | added | holmrenser | Just out of curiosity: can you elaborate on how BLAT 'provided the easiest means to access information on the actual alignment blocks (with the smallest amount of parsing)'? What about blast HSPs? | |
| May 18, 2017 at 9:11 | history | asked | Sam Nicholls | CC BY-SA 3.0 |