https://sourceforge.net/p/integrate-fusion/wiki/alignment-tools/Recent changes to alignment-toolsenThu, 28 May 2015 14:45:08 -0000https://sourceforge.net/p/integrate-fusion/wiki/alignment-tools/<div class="markdown_content"><pre>--- v2 +++ v3 @@ -41,5 +41,5 @@ Integrate fusion hg19.fa ensembl.txt bwts/ 1.mapped.bam 2.not-mapped.bam INTEGRATE 0.2.0 takes mapped encompassing reads, soft-clipped and/or hard-clipped spanning reads, and reads serve as anchor (i.e mate not mapped) from 1.mapped.bam. INTEGRATE 0.2.0 takes the not mapped mates from 2.not-mapped.bam. -We have tested TopHat2, GSNAP, and STAR. +We have tested running INTEGRATE 0.2.0 with BAMs from TopHat2, GSNAP, and STAR. </pre> </div>JinThu, 28 May 2015 14:45:08 -0000https://sourceforge.net2512f6c35b5e905185226b322c3d997843474947https://sourceforge.net/p/integrate-fusion/wiki/alignment-tools/<div class="markdown_content"><pre>--- v1 +++ v2 @@ -0,0 +1,45 @@ +From version 0.2.0, INTEGRATE is supporting more RNA-Seq reads alignment tools. For example, GSNAP and STAR. +--------------- + +example commands of running GSNAP: + +~~~~~~~~~~~~~~~~~ +gsnap -d hg19 -D hg19.gmap_index/ --format=sam --nthreads=12 -s hg19.splicesites.iit 1.fastq 2.fastq &gt; gsnap.sam + +samtools view -Sb -o gsnap.bam gsnap.sam + +samtools sort gsnap.bam gsnap.sort + +samtools index gsnap.sort.bam +~~~~~~~~~~~~~~~~~ + +example commands of running STAR: + +~~~~~~~~~~~~~~~~~~~ +STAR --runThreadN 12 --genomeDir hg19.star.index/ --readFilesIn 1.fastq 2.fastq --outFileNamePrefix star --chimSegmentMin 18 + +samtools sort star.chimeric.mapped.bam star.chimeric.mapped.sort + +samtools index star.chimeric.mapped.sort.bam +~~~~~~~~~~~~~~~~~~~ + +example command of running INTEGRATE using BAMs from GSNAP: + +~~~~~~~~~~~~~~~~~~~ +Integrate fusion hg19.fa ensembl.txt bwts/ gsnap.sort.bam gsnap.sort.bam wgs.tumor.bam wgs.normal.bam +~~~~~~~~~~~~~~~~~~~ + +example command of running INTEGRATE using BAMs from STAR: + +~~~~~~~~~~~~~~~~~~~ +Integrate fusion hg19.fa ensembl.txt bwts/ star.chimeric.mapped.sort.bam star.chimeric.mapped.sort.bam wgs.tumor.bam wgs.normal.bam +~~~~~~~~~~~~~~~~~~~ + +Note +---- +for a command such as: +Integrate fusion hg19.fa ensembl.txt bwts/ 1.mapped.bam 2.not-mapped.bam +INTEGRATE 0.2.0 takes mapped encompassing reads, soft-clipped and/or hard-clipped spanning reads, and reads serve as anchor (i.e mate not mapped) from 1.mapped.bam. INTEGRATE 0.2.0 takes the not mapped mates from 2.not-mapped.bam. + +We have tested TopHat2, GSNAP, and STAR. + </pre> </div>JinThu, 28 May 2015 14:44:18 -0000https://sourceforge.netdca8fcc85aeb9f22acd5997b94fb46f70e2d5436https://sourceforge.net/p/integrate-fusion/wiki/alignment-tools/JinThu, 28 May 2015 14:17:40 -0000https://sourceforge.net27c8096ff7ac29f94c0769b9667a5de85258ca79