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Old 03-21-2012, 10:05 PM   #1
ritzriya
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Arrow BLASR output - what does each column mean?

Hi all,

I wanted to understand the meanings of each column in the BLASR output, which looks like:

Quote:
msherri_s1_p0/20/0_269 gi|170079663|ref|NC_010473.1| 0 -1119 87.3333 4158698 4158998 4686137 6 269 269 0
msherri_s1_p0/20/0_269 gi|170079663|ref|NC_010473.1| 1 -157 59.5855 3023879 3024050 4686137 4 169 269 0
I understand that first column denotes the query name and second column denotes the subject genome (e.coli in this case). What about other columns? Does anyone have an idea?
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Old 03-25-2012, 10:10 PM   #2
ritzriya
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Hi all,

I have got the answer to this doubt. If you use -header while running BLASR, you will get the header names onto the output file. Sorry for posting the query too soon. :-)
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Old 11-20-2012, 03:51 AM   #3
cnluzon
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Hi all,

I have one further question on this topic. I see the header in BLASR standard and extended output, but there are a couple of fields I don't know what they mean and I cannot find them in any documentation.

For instance:
qname tname score pctsimilarity qstrand qstart qend qseqlength tstrand tstart tend tseqlength mapqv ncells clusterScore probscore numSigClusters
readX targetFileY -500 100 0 0 100 100 0 2037 2137 4950 254 2067 -17.3093 0 1

Specially, I do not know what the ncells field means.
Also, fields clusterScore, probscore, numSigClusters are unclear since I would need to know how they are calculated.

Do anyone know what these mean or any place where there is more detail about these? Thank you
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Old 02-04-2013, 09:45 PM   #4
mchaisso
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Rather, it's the number cells used in dynamic programming, used to track performance of some of the variable-width banding methods. Nobody should be interested in this (and if I had the power of Apple, I would just remove it and let people update their parsing accordingly).

-mark

Quote:
Originally Posted by jbingham View Post
Not sure if you're still interested in this...

ncells = Number of SMRT Cells
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Old 02-04-2013, 09:47 PM   #5
mchaisso
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These have no meaning to people, and should be removed. Sorry they are still there.

best,
-mark


Quote:
Originally Posted by cnluzon View Post
Hi all,

I have one further question on this topic. I see the header in BLASR standard and extended output, but there are a couple of fields I don't know what they mean and I cannot find them in any documentation.

For instance:
qname tname score pctsimilarity qstrand qstart qend qseqlength tstrand tstart tend tseqlength mapqv ncells clusterScore probscore numSigClusters
readX targetFileY -500 100 0 0 100 100 0 2037 2137 4950 254 2067 -17.3093 0 1

Specially, I do not know what the ncells field means.
Also, fields clusterScore, probscore, numSigClusters are unclear since I would need to know how they are calculated.

Do anyone know what these mean or any place where there is more detail about these? Thank you
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Old 02-05-2013, 03:26 AM   #6
cnluzon
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Ok, I was wondering if there was anything I was missing. Thank you for your help
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Old 01-18-2014, 10:08 AM   #7
oakeley
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I had a quick question about the SAM output of BLASR. What flags are needed to make a regular SAM file (specifically with a proper SAM header and the sequences in the output not just the coordinates).

Thanks

Edward
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Old 01-20-2014, 10:52 PM   #8
ACEnglish
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The -sam parameter.
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