Wednesday, August 24, 2011

Extract insert size of paired-end reads from Cufflinks output

The new version of Cufflinks tries to estimate the mean and std value of paired-end read insert size automatically. Sometimes we need to extract such information to check our sequencing data. Here I wrote a simple script to search Cufflinks outputs.

The script is written in Python. The implementation is easy: search for key words (like "Estimated Mean", etc) in log files. The usage is as follows:


This script extracts insert size information from Cufflinks logs.
Usage: getinsertsize [cufflinks log file]
Note: you may specify different log files using filename wildcards.



Sample output:

File    MapMass ReadLength      Mean    Std
cufflinksinvoke.sh.e2148442     34108402.45     85      150.35  19.18
cufflinksinvoke.sh.e2148443     31007287.59     85      155.19  17.45
cufflinksinvoke.sh.e2148444     37286038.02     85      123.87  25.60

Source code:



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