bam2fpkc
Project description
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Overview
=========
This script works out how many reads are mapping to each contig OR if you ask it
nicely, it will find the median number of reads mapping to all contigs in your bins.
The number of fragments mapping to any contig is normalised for contig length to give
the average number of fragments mapping per 1000 bases of contig or.. fpkc
Installation
=========
Should be as simple as
pip install bam2fpkc
Data preparation and running bam2fpkc
=========
You'll always need a set of contigs and a corresponding set of sorted indexed bam files.
Then you just need to decide if you want to get fpkc values for a set of contigs or a
the median fpkc for all contigs in your bins.
Contigs:
Options are in flux, use:
bam2fpkc contig -h
for more info...
Bins:
For this you'll need a 'bins file'. This is a TAB separated file of the form
cid -> bid
Currently, the cid MUST exactly match the contig headers in the fasta file AND
all cids must be accounted for. IE. unbinned contigs should be assigned to bin 0
or some other sensible assignment.
Otherwise use:
bam2fpkc bin -h
for more info...
Licence and referencing
=========
Project home page, info on the source tree, documentation, issues and how to contribute, see http://github.com/minillinim/bam2fpkc
This software is currently unpublished. Please contact me at m_dot_imelfort_at_uq_dot_edu_dot_au for more information about referencing this software.
Copyright © 2013 Michael Imelfort. See LICENSE.txt for further details.
.
. 888 .d8888b. .d888 888
. 888 d88P Y88 d88P" 888
. 888 88 888 888
. 88888b. 8888b. 88888b.d88b. .d88 888888 88888b. 888 888 .d8888b
. 888 "88b "88b 888 "888 "88b .od888P" 888 888 "88b 888 .88P d88P"
. 888 888 .d888888 888 888 888 d88P" 888 888 888 888888K 888
. 888 d88P 888 888 888 888 888 888" 888 888 d88P 888 "88b Y88b.
. 88888P" "Y888888 888 888 888 88888888 888 88888P" 888 888 "Y8888P
. 888
. 888
. 888
.
Overview
=========
This script works out how many reads are mapping to each contig OR if you ask it
nicely, it will find the median number of reads mapping to all contigs in your bins.
The number of fragments mapping to any contig is normalised for contig length to give
the average number of fragments mapping per 1000 bases of contig or.. fpkc
Installation
=========
Should be as simple as
pip install bam2fpkc
Data preparation and running bam2fpkc
=========
You'll always need a set of contigs and a corresponding set of sorted indexed bam files.
Then you just need to decide if you want to get fpkc values for a set of contigs or a
the median fpkc for all contigs in your bins.
Contigs:
Options are in flux, use:
bam2fpkc contig -h
for more info...
Bins:
For this you'll need a 'bins file'. This is a TAB separated file of the form
cid -> bid
Currently, the cid MUST exactly match the contig headers in the fasta file AND
all cids must be accounted for. IE. unbinned contigs should be assigned to bin 0
or some other sensible assignment.
Otherwise use:
bam2fpkc bin -h
for more info...
Licence and referencing
=========
Project home page, info on the source tree, documentation, issues and how to contribute, see http://github.com/minillinim/bam2fpkc
This software is currently unpublished. Please contact me at m_dot_imelfort_at_uq_dot_edu_dot_au for more information about referencing this software.
Copyright © 2013 Michael Imelfort. See LICENSE.txt for further details.
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