Wiki - User contributions [en]

User:Tlassmann/Delve

2011-01-17T03:47:55Z

Tlassmann:

== News ==

More to come soon.

== Purpose ==

Delve is a probabilistic aligner which is capable of mapping Helicos reads accurately despite the high error rate.

== Method ==

[[File:Delve User Manual.pdf]]

== Input ==

Sequences in fasta / fastq format

== Output ==

Alignments inn SAM/BAM format.

User:Tlassmann/Delve

2011-01-17T03:47:06Z

Tlassmann: Created page with '== News == More to come soon. == Purpose == Delve is a probabilistic aligner which is capable of mapping Helicos reads accurately despite the high error rate. == Method ==…'

== News ==

More to come soon.

== Purpose ==

Delve is a probabilistic aligner which is capable of mapping Helicos reads accurately despite the high error rate.

== Method ==

[[File:Delve User Manual.pdf]]

== Input ==

Delve mapping files in bam format.

== Output ==

Cluster file in BED format.

File:Delve User Manual.pdf

2011-01-17T03:43:47Z

Tlassmann: Delve user manual.

Delve user manual.

User:Tlassmann/rRNA filtering

2011-01-17T03:41:54Z

Tlassmann: Created page with '== Purpose == Remove reads corresponding to rRNA from Helicos CAGE datasets. == Method == Since the error rate of Helicos is high and includes many insertion / deletion errors…'

== Purpose ==

Remove reads corresponding to rRNA from Helicos CAGE datasets.
== Method ==

Since the error rate of Helicos is high and includes many insertion / deletion errors, the only viable option was to match sequences against rRNA sequences (U13369.1) using a non-heuristic alignment algorithm. Due to the amount of data a SSE parallelized version of Myers bit-parallel algorithm was implemented.

All reads matching the reference rRNA sequences with up to 2 errors are discarded at this step.
== Input ==

Helicos fasta sequences.

== Output ==

Reads not matching rRNA.

User:Tlassmann/clustering

2011-01-14T08:55:49Z

Tlassmann:

== 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 ==
[[File:clusteringPipeline.png|frameless|caption]] 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.

==== bedToCtss.sh ====

#!/bin/sh

INFILE=out/CNhs10333.2855-61D3.nobarcode.truesingle.bed.gz
INFILE=

function usage()
{
cat <<EOF
usage: $0 -i MAPPING.bed.gz
EOF
exit 1;
}

while getopts i:s: opt
do
case ${opt} in
i) INFILE=${OPTARG};;
*) usage;;
esac
done

if [ "${INFILE}" = "" ]; then usage; fi

gunzip -c ${INFILE} \
| awk 'BEGIN{OFS="\t"}{if($6=="+"){print $1,$2,$5}}' \
| sort -k1,1 -k2,2n \
| /quality_control/development/bin/groupBy -i stdin -grp 1,2 -opCols 3 -ops count \
| awk 'BEGIN{OFS="\t"}{print $1,$2,$2+1, $1":"$2".."$2+1",+" ,$3,"+"}'

gunzip -c ${INFILE} \
| awk 'BEGIN{OFS="\t"}{if($6=="-"){print $1,$3,$5}}' \
| sort -k1,1 -k2,2n \
| /quality_control/development/bin/groupBy -i stdin -grp 1,2 -opCols 3 -ops count \
| awk 'BEGIN{OFS="\t"}{print $1,$2-1,$2, $1":"$2-1".."$2",-" ,$3,"-"}'

== 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.

User:Tlassmann/clustering

2011-01-14T08:50:42Z

Tlassmann:

User:Tlassmann/clustering

2011-01-14T08:50:29Z

Tlassmann: /* Output */

User:Tlassmann/clustering

2011-01-14T08:43:25Z

Tlassmann: /* Output */

File:ClusteringPipeline.png

2011-01-14T08:40:44Z

Tlassmann: Image of basic CAGE clustering pipeline

Image of basic CAGE clustering pipeline

User:Tlassmann/clustering

2011-01-14T08:35:14Z

Tlassmann: Created page with '== 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. Expre…'

User:Tlassmann

2011-01-14T08:34:05Z

Tlassmann: Blanked the page

User:Tlassmann

2011-01-14T08:29:37Z