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Galaxy

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Wortcflow Shared Data- Yisualization - Help-r User

Tools

KOJ, nuwinii

NGSl P-N-Ą A»aty5b NGS: SAMtoob

eader repiace

header in a SAM/BAM dataset

AddCofnmentsTgBam add comments to BAM dataset

SamTofasto extract reads and qualities from SAM/BAM dataset and convert to fastq

r

V

Downsąmplę SAM/BAM Downsample a file to retain a subset of the reads

MarkDudicates examine aligned records In BAM datasets to locate duplicate molecules

RęordęrSąm reorder reads to match ordering in reference seguences

ReyeitSam revert SAM/BAM datasets to a previous State

EflimateUtKarY.Comrigrihr assess sequence library complexity from read sequences

SortSam sort Sam/bam dataset

WdOffiepl.aceReadGrotiEs add or replaces read group information

£2llgaRnąS£flMfilrię§ coiect metrics about the aignment of RNA to various functional dasses of loci in the genome

deanSam perform SAM/BAM

/■ MarkDuplicates examlne aligned records in BAM datasets to locate duplicate molecules (Galaxy Tool version 1.126.0)

- Options

/BAM dataset or dataset collection

•ma tri mat) I •mat J

2: Map with BWA-MEM on data 7 and data 6 (mapped reads In BAM form 11: Map with BWA-MEM on data 5 and data 4 (mapped reads In BAM format) 0: Map with BWA-MEM on data 3 and data 2 (mapped reads In BAM format

.1. This is a batch modę input field. A separate job will be triggered for each dataset. If empty, upload or import a SAM/BAM dataset

Comment + Insert Comment

You can provide multiple comments

do not write duplkates to the output file Instead of writing them with appropriate flags set

^ Yes^lo

^•■•^.DUPLICATES; default-False Assunie the input file is already sorted

Yes No

ASSUME_SORTED; default-True

The scoring strategy for choosing the non-duplicate aniong candidotes

| SUM_0F_BASE_QUA1ITIES

DUPUCATE_SCORING_STRATEGY; default = SUM_OF_BASE_QUAimES

Regular expresslon that can be used to parse read nanieś In the incoming SAM/BAM dataset

|[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([O-91+).*.

READ_NAME_REGEX; Read names are parsed to extract three variaWes: tile/region, x coordnate and y coordinate. These values are used to estimate the ratę of optical duplication in order to give a morę accurate estimated library size. See help below for morę info; default=[a-zA-Z0-9]+: [0-9]:([0-9]f):([0-9M:([0-9]-O.-.

The maximum offset between two duplicte clusters in order to consider them optical duplkates

| ioo 11    g    -)

0PT1CAL_DUPUCATE_P1XEL_DISTANCE; default-100 Select yalidatioo stringency

Lenient

Setting stringency to SILENT can improve performance when Processing a BAM file in whkh variabłe-length data (read, qualities, tags) do not otherwise need to be decoded.