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Last active October 25, 2022 06:15
Estimating NGS paired-end read insert size (or fragment length) from SAM/BAM files
#!/usr/bin/env python
Automatically estimate insert size of the paired-end reads for a given SAM/BAM file.
Usage: <SAM file> or samtools view <BAM file> | -
Author: Wei Li
Copyright (c) <2015> <Wei Li>
davidliwei /
Created August 24, 2011 18:34
This script extracts insert size mean and std, mass of mapped read information from Cufflinks log outputs.
#!/bin/env python3
import os
import re
import sys
if len(sys.argv)<2:
print('This script extracts insert size information from Cufflinks logs.',file=sys.stderr);
print('Usage: getinsertsize [cufflinks log file]',file=sys.stderr);
print('Note: you may specify different log files using filename wildcards.',file=sys.stderr);
davidliwei /
Created August 18, 2011 23:44
Converting Cufflinks predictions (.GTF) into .BED annotations
#!/usr/bin/env python3
''' converts GTF file to BED file.
Usage: {OPTIONS} [.GTF file]
Nov.5th 2012:
1. Allow conversion from general GTF files (instead of only Cufflinks supports).
2. If multiple identical transcript_id exist, transcript_id will be appended a string like "_DUP#" to separate.