BLASR output - what does each column mean?

[ritzriya]

Hi all,

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

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?

[ritzriya]

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. :-)

[cnluzon]

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

[mchaisso]

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

Not sure if you're still interested in this...

ncells = Number of SMRT Cells

[mchaisso]

These have no meaning to people, and should be removed. Sorry they are still there.

best,
-mark

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

[cnluzon]

Ok, I was wondering if there was anything I was missing. Thank you for your help

[oakeley]

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

[ACEnglish]

The -sam parameter.