# ATLAS / Sequence Data Processing Tools: splitRGbyLength

## Input

• A BAM file

• A .txt file :

Create a .txt file containing the names of the single-end read groups and their maximum cycle number (separated by any whitespace). The read group names can be found in the header of your BAM file but note that 'ID:' is not part of the read group name. If you do not know at what maximum cycle number the genome was sequenced at you can find the maximum read length in the BAM file with our task BAMDiagnostics.

Example:

## Output

• A BAM file with suffix "_splitRG.bam" :

It containing the originial read group and a new read group. The original readgroup contains the reads that are of the specified maximum read length, while the read group with suffix _truncated contains the reads that are of a smaller read length than the specified maximum.

## Usage Example

./atlas task=splitRGbyLength bam=example.bam readGroups=singleEndReadgroups.txt verbose


## Specific Arguments

• readGroups : Specify the file with list of single-end read groups that should be split according to their maximum read length.
• allowForLarger : Allow reads that are larger than maximum length to be added to the "_truncated" read group. This is useful if you think there might be an adapter contamination.

## Engine Parameters

Engine parameters that are common to all tasks can be found here.

Updated