Hi,
I've started using SOAPsplice to see if it is a usefull spliced aligner.
The tool ran without problems and I'm left with 3 files.
a .out file
a .2Segs file
a .junc file
the .junc file only contains info about the junctions, and how many times the junctions were skipped, so that's just a text file.
I have opened the files, and I understand the information.
It contains almost the same data as a SAM file
(name, length of segments, indels, what strand it's on, ...)
But my question is:
How can I visualise this data?
If it was a BAM file I could view it with a genomeviewer of some sort, and see where all the reads aligned, but I can't use a .out file.
So, what type of file is this, or alternatively, how do I process these files?
Here's a short sample of the file:
I've started using SOAPsplice to see if it is a usefull spliced aligner.
The tool ran without problems and I'm left with 3 files.
a .out file
a .2Segs file
a .junc file
the .junc file only contains info about the junctions, and how many times the junctions were skipped, so that's just a text file.
I have opened the files, and I understand the information.
It contains almost the same data as a SAM file
(name, length of segments, indels, what strand it's on, ...)
But my question is:
How can I visualise this data?
If it was a BAM file I could view it with a genomeviewer of some sort, and see where all the reads aligned, but I can't use a .out file.
So, what type of file is this, or alternatively, how do I process these files?
Here's a short sample of the file:
Code:
113 ERR008661.113 HWI-EAS-249:8:1:6:1240 length=76 3,6 14,62 - fwd 4,9 24314529,3558 0,1 T->75A2 119 ERR008661.119 HWI-EAS-249:8:1:6:1091 length=76 1,1 55,21 + fwd 3,7 25613551,22003337 1,1 C->54G-27 G->71C-27 143 ERR008661.143 HWI-EAS-249:8:1:6:1431 length=76 150,1 13,63 - fwd 8,11 25794407,11406025 1,0 A->0C-8 146 ERR008661.146 HWI-EAS-249:8:1:6:766 length=76 1,387 63,13 + fwd 7,1 2136065,1601872 0,1 A->63G-27 158 ERR008661.158 HWI-EAS-249:8:1:6:895 length=76 4,11 61,15 + fwd 9,1 6038,4328985 0,1 C->64G-27 165 ERR008661.165 HWI-EAS-249:8:1:7:1526 length=76 211,1 14,62 - fwd 5,7 23911678,2546089 1,1 A->0C-27 A->75G0