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Last pushed: a year ago
Short Description
Step1 for hictool (GITAR), a Hi-C data analysis tool
Full Description

This one aligns fastq files to the human genome and processes the alignment files according to the hictool (GITAR) procedure.

Arguments: bowtie_index(tgz) fastq1 fastq2 outdir
fastq1 and fastq2 represent the two mates of the same sample. The output bam files will be put in outdir.

Run example:
docker run -v /home/ec2-user/files/:/data/:rw duplexa/hictool-fastq2bam /data/hg19.bowtieIndex.tgz /data/GM12878_SRR1658581_1pc_1_R1.fastq /data/GM12878_SRR1658581_1pc_1_R2.fastq /data

==Old versions==

v1:
Arguments: fastq1 fastq2 outprefix
fastq1 and fastq2 represent the two mates of the same sample. The output bam file names will start with outprefix. Both files and the outprefix should include the full path, assuming that they're in /data/. The host directory that contains the input files should be mounted as /data/.
Hg19 assumed.

Run example:
docker run -v /home/ec2-user/files/:/data/:rw duplexa/hictool-fastq2bam /data/GM12878_SRR1658581_1pc_1_R1.fastq /data/GM12878_SRR1658581_1pc_1_R2.fastq /data/GM12878_SRR1658581

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Owner
duplexa

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