Hi,
Could anyone point me out to the meaning of the different fields in a PacBio Fastq sequence name.
Example:
@m141104_013014_42198_c100718132550000001823144805141512_s1_p0/93/116_1715 0.82 24
ATAGCTGATCGTGAC....
....
@m141104_013014_42198_c100718132550000001823144805141512_s1_p0/93/1768_3406 0.82 24
ATGCTAGTACG.....
What does it mean that both sequence have the same name prefix (@m141104_013014_42198_c100718132550000001823144805141512_s1_p0/93/)
Any pointers would be appreciated.
Madi
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apt.university
m140415_143853_42175_c100635972550000001823121909121417_s1_p0/553/3100_11230 0.99 24
└1┘└─────2─────┘└──3─┘└────────────────4────────────────┘└5┘└6┘└7┘└────8────┘└─9─┘└10┘
m = *movie(yymmdd_hhmmss)p0, X0 when using expired reagents)start_stop using polymerase read coordinates)
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jkaralius •
@jkaralius That's exactly what I needed -- thanks a lot.
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apt.university
PacBio SMRT-sequencing uses a circularized DNA template fragments for sequencing. Depending on the length of the fragment, the polymerase loops along this template multiple times. The produces a read with actual multiple segments, called subreads, each representing (at least a part) of the actual template.
@m...512_s1_p0/93 corresponds to a read of one circularized fragment.
@m...512_s1_p0/93/116_1715 and @m...512_s1_p0/93/1768_3406 correspond to two subreads from the same template, with the two numbers after the second / giving you the coordinates of the subread relative to the original read.
The orientation of subsequent subreads alternates (forward - reverse-complement - forward - ...). If you align them, you can see the similarities.
For more details, also about the first parts of the read IDs, have a look for example at SMRT-sequencing workflow and Understanding-PacBio-transcriptome-data (it says transcriptome, but is the general explanations are true for genomic sequencing as well)
@thackl the reason I was asking about the name is that I wanted to know which part represented the ZMW number so that I can know which reads are from the same insert. Your links were helpful though. Thanks for taking the time to post an answer!
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apt.university
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