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WGLab / RepeatHMM

a hidden Markov model to infer simple repeats from genome sequences
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How to use paired end fastq reads for RepeatHMM #28

Closed amrita1983 closed 4 years ago

amrita1983 commented 5 years ago

Hi,

I am trying to find out HTT repeats in known sample, but when I am using the bam file generated using BWA local mode, it is not showing any repeat at all. I am very surprised with the output. I thought of using the fastq file directly, but did not find out how to use paired end illumina WGS data for it. Command: python2 repeatHMM.py BAMinput --Onebamfile HD_aligned.sorted.bam --hg hg19 --hgfile /home/ngs/Downloads/RepeatHMM/bin/ref/hg/hg19.fa --repeatName all

It is extremely urgent to get the result for me as I have a conference next week it would be great if you can help me.

liuqianhn commented 5 years ago

Hi @amrita1983 , RepeatHMM is not designed to work on paired end reads. you can add --GapCorrection 0 --FlankLength 15 --MinSup 3 --SplitAndReAlign 0 with a bam so that RepeatHMM might output some repeats, but paired end information is not used and each read is considered separately.

amrita1983 commented 5 years ago

Thank you for the reply, but still the tool is not able to detect any repeat expansion from the BAM file using the options that you have mentioned. I will try using fastq file once.

liuqianhn commented 5 years ago

If you want, could you please get a bam for a specific repeat region and the repeat region information and the bam file to me for testing? Thank you.

liuqianhn commented 4 years ago

Closed due to no recent activities.