User:Tlassmann/clustering
Purpose
Provide basic F3 style clustering.
Method
For each library, Helicos CAGE tag mappings with Delve quality of at least 10 were clustered into CTSS:s. Expression was calculated as tags per million (TPM) and CTSS:s with at least 1 TPM expression were clustered using single linkage clustering (separate on each strand) of tags spaced at most 20 bp.
Input
Delve mapping files in bam format.
Output
Cluster file in BED format.
Details
This is a graphical representation of the basic clustering pipeline.
minimum_mapping_quality
Version
1.0
Command
/quality_control/development/bin/samtools view -b -q [quality] [input] > [output]
Parameter
Key Value quality 10
Output
to bamToBed input
Description
Remove low quality mapping below QV of [quality] using samtools view command. samtools version is 0.1.8 (r613).
bamToBed
Version
1.0
Input
from minimum_mapping_quality output
Command
/quality_control/development/bin/bamToBed -i [input] | gzip > [output]
Parameter
none
Output
to bedToCtss input
Description
v2.10.0 Aaron Quinlan Converts BAM alignments to BED6 or BEDPE format.
bedToCtss
Version
1.0
Input
from bamToBed output
Command
/quality_control/development/bin/bedToCtss.sh -i [input] | gzip > [output]
Parameter
none
Output
to cluster_ctss input
Description
Program by Erik Arner.
cluster_ctss
Version
1.0
Input
from bedToCtss output
Command
/quality_control/development/bin/cluster_ctss.pl [input] --min_TPM [minimum_TPM] > [output]
Parameter
Key Value minimum_TPM 1
Output
to output
Description
Program by Erik Arner.
