Question: Scripture : Paired-End Data
gravatar for Nicolas Rosewick
8.3 years ago by
Belgium, Brussels
Nicolas Rosewick9.0k wrote:


I've a little problem to understand the scripture command line :

So I've the accepted_hits.bam for all my samples. So I have to merge all the bam files into one big bam file before running scripture. In the help file there is two alignment file param :

-alignment --pairedEnd

Which one do I have to use to input the merged bam file ?

Here's the help file :

 -alignment <Alignment file in BAM, SAM or Alignemnt format> 
 -maskFileDir <Mask File directory> 
 -out <Output file name>
 -windows <Comma separated list of windows to evaluate>
 -sizeFile <Chromosome size file>  
 Optional arguments: 
 -trim <Include this flag if trimming of the ends of windows based on read coverage  is desired this is expensive> 
 -alpha <Desired FDR>
 one of -chr <Chromsomosome to segment> or -chrSequence <Necessary to filter spliced reads by splice site information. Notice that this is only compatible with region files that contain regions of only one chromosome> -dontFilterCanonicalSplice
 -start <To segment only a subregion of the chromosome include its start> -end <To segment only a subregion of the chromosome include its end>
 -minSpliceSupport <Minimum count to support splice reads, default is 1> 
 -pairedEnd <Paired end alignment files> -strandSpecificReads <Strand specific alignment file> -scoreRegions <Full BED to score> -upWeightSplices -lambda <If a prior background expectation for number of reads per base exists> -exons <BED file of exons> -introns <Introns and counts>

Task: AddPairs -  Uses a paired end alignment to tune graph 
    -in <Graph in .dot format. Standard input is assumed> 
    -pairedEnd <Paired end information (as in previous task), in single line BED format>
     -maskFileDir <Directory containing mask files for the genome> 
    -chr <Chromosome (only a chromosome at a time is supported at this point)> 
    -sizeFile <Chromosome size file> 
    -out <Output file name>

Task: score -  Computes several expression related scores for a set of annotations -in <Full BED file with annotations to score> 
    -alignment <Alignment file in BAM, SAM or Alignemnt format> 
    -sizeFile <Chromosome size file> 
    -out <Output file name> 
     -maskFileDir <Mask File directory>



ADD COMMENTlink written 8.3 years ago by Nicolas Rosewick9.0k
gravatar for Vikas Bansal
8.3 years ago by
Vikas Bansal2.4k
Berlin, Germany
Vikas Bansal2.4k wrote:

I just read about this tool and will share what I understood. So you can read a walkthrough example here.So if you have paired end data, then you have option to use pairedEnd argument. This argument will take files generated by makePairedFile task.

From the link- So if you have paired end data, you will have 2 files for each "accepted_hits.sorted.sam". First you have to use makePairedFile task-

>> java -Xmx4000m -jar scripture.jar -task makePairedFile -pair1 tophat_out_SRR039999_1/accepted_hits.sorted.sam -pair2 tophat_out_SRR039999_2/accepted_hits.sorted.sam -out SRR039999.paired.sam -sorted
>> java -Xmx4000m -jar scripture.jar -task makePairedFile -pair1 tophat_out_SRR040000_1/accepted_hits.sorted.sam -pair2 tophat_out_SRR040000_2/accepted_hits.sorted.sam -out SRR040000.paired.sam -sorted
>> java -Xmx4000m -jar scripture.jar -task makePairedFile -pair1 tophat_out_SRR040001_1/accepted_hits.sorted.sam -pair2 tophat_out_SRR040001_2/accepted_hits.sorted.sam -out SRR040001.paired.sam -sorted

and then combine these files-

>> cat SRR039999.paired.sam SRR040000.paired.sam SRR040001.paired.sam > all_alignments.paired.sam

and then sort and index. So now this file "all_alignments.paired.sorted.sam" will be used in pairedEnd argument. and for -alignment parameter you will simple combine your bam files-

>> cat tophat_out_SRR039999_1/accepted_hits.sorted.sam tophat_out_SRR039999_2/accepted_hits.sorted.sam tophat_out_SRR040000_1/accepted_hits.sorted.sam tophat_out_SRR040000_2/accepted_hits.sorted.sam tophat_out_SRR040001_1/accepted_hits.sorted.sam tophat_out_SRR040001_2/accepted_hits.sorted.sam > all_alignments.sam

Sort and index.Now this "all_alignments.sorted.sam" will be used in -alignment parameter.

So they used this command in example-

>>java –jar scripture.jar –alignment all_alignments.sorted.sam –out chr19.scriptureESTest.segments –sizeFile mm9.sizes –chr chr19 –chrSequence chr19.fa -pairedEnd all_alignments.paired.sorted.sam
ADD COMMENTlink written 8.3 years ago by Vikas Bansal2.4k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1454 users visited in the last hour