Small RNA Transfrags from CSHL

Small RNA reads from Cold Spring Harbor Lab (CSHL) were assembled into transfrags by merging overlapping reads. In order to minimize ambiguity from reads that have the potential to map to multiple genomic loci, only the uniquely mapping reads were used to generate transfrags. The BED6+ format files are based on, but not generated directly by, the "intervals-to-contigs" Galaxy tool written by Assaf Gordon (gordon@cshl.edu) in the Hannon lab at CSHL. Below is a description of the columns in this format, and how each column is calculated.

Output Columns

(Bed-style transfrag information)

(Additional Sequences Information)

(Additional Reads Information)

(Additional Intervals Information)


Concrete Example

Assume the following intervals over an imaginary chromosome chr1:

chr1        100     132     4
chr1        110     142     3
chr1        130     160     7
chr1        170     201     3
chr1        190     225     1

Plotting these intervals:

./static/images/intervals_to_transfrags.png

These intervals cover two transfraguous regions (marked in red): 100-160 and 170-225.

The output file will contain two lines (one for each transfrag):

chr1      100     160     transfrag-1     1000     +     60      3       14      1       3       1.6     1       2       2       4       14      7.35    7       7       7       5       100,110,130,133,143     10,20,3,10,17   1,2,3,2,1       4,7,14,10,7     441
chr1      170     225     transfrag-2     286      +     55      2       4       1       2       1.21818 1       1       1       1       4       2.38182 1       3       3       3       170,190,202             20,12,23        1,2,1           3,4,1   131

The rest of the explanation will focus on the first transfrag only:

(transfrag information):

(sequence-count information):

(reads-count information):

(significant regions information):