This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Hi-C data alignment with star

Dear community,

Does anyone has experience with aligning data using star aligner? It would be very kind of you to share the syntax that you used or have a look at mine and point corrections (chimeric reads alignments etc)

As reads from both strands need to be mapped seperately, I am using following command:

STAR --genomeDir /data/genomes/ --readFilesIn /data/raw/HiREAD/HiC/T-Rep1_R2_001.fastq.gz --readFilesCommand gunzip -c --alignIntronMax 1 --alignIntronMin 2 --outFilterMultimapNmax 1 --runThreadN 8 --outFileNamePrefix T_Rep1_L2

Kindly let me know, if I am missing something here :)

bwa takes a lot of time .... a lot

Thank you

star hi-c
• 4,557 views • link
updated by Gautier Richard Gautier Richard • written by Dataminer Dataminer

Hi Santosh,

This is working fine no error, I will have a look at the link, thank :)

• 1 views • link
written by Dataminer Dataminer

BWA takes a long time because Hi-C datasets are large. What is your definition of "long", and how many CPUs did you use (full command line), what is your hardware? There are probably things one can optimize if you share your code.

• 1 views • link
written by ATpoint ATpoint

Definition: 5 days of processing on HPC, with 12 threads and 132 Gb RAM. I understand that Hi-C data is huge and will take time, however 5 days is a lot :)

• 1 views • link
written by Dataminer Dataminer

How many reads in the dataset?

• 1 views • link
written by ATpoint ATpoint

1 answer

For aligning Hi-C reads, you could try this command line with BWA (12 cores):

bwa mem -A1 -B4 -E50 -L0 -t 12 bwa_index.fa sequences_R1.fastq bwa mem -A1 -B4 -E50 -L0 -t 12 bwa_index.fa sequences_R2.fastq

This is what is used in the Snakepipes pipelines: https://github.com/maxplanck-ie/snakepipes/

Maybe your BWA alignment took longer than it should because of different parameters? Snakepipes is using 15 cores for that command and usually take less than a day to run. Even for deeply sequenced samples it took far less than 5 days.

With that command-line I don't see the point of using STAR for mapping Hi-C reads.

• 1 views • link
written by Gautier Richard Gautier Richard

Hi, I was using exactly the same bwa mem -A1 -B4 -E50 -L0 -t 12 ref.fa file1.fastq Btw I have plant genome polyploidy

• 1 views • link
written by Dataminer Dataminer

For STAR I found this from the HIPPIE package for Hi-C data, perhaps it can help:

https://github.com/yihchii/hippie/blob/master/cmd/starMappingToBam.sh

So maybe you could grab some additional parameters from those? --outFilterMultimapNmax 1 and --alignIntronMax 1 you already had.

 --outFilterMultimapNmax 1 \
 --outFilterMismatchNovermax 0.04 \
 --scoreGapNoncan 0  --scoreGapGCAG 0  --scoreGapATAC 0 \
 --alignIntronMax 1 \
 --chimSegmentMin ${ChimSegMin} \
 --chimScoreJunctionNonGTAG 0
• 1 views • link
written by Gautier Richard Gautier Richard

After further research I saw that STAR, when used with several CPUs, will scramble the reads order. Hi-C tools are usually waiting for properly ordered files in order to build matrices, I think for a correct pairing of the individual mapped files.

For that you can for example use ReorderSam from Picard. Of course it needs testing and it might depend on the Hi-C suite you use afterwards to build matrices (HiCExplorer is taking R1.bam and R2.bam as input of hicBuildMatrix for example, I believe that other suites might take paired bam files as input).

• 1 views • link
written by Gautier Richard Gautier Richard

Log in to answer this question.

More posts like this