scottzijiezhang / m6a-seq_analysis_workflow Goto Github PK
View Code? Open in Web Editor NEWA pipeline to process m6A-seq data and down stream analysis.
A pipeline to process m6A-seq data and down stream analysis.
Hi Zijie,
I notice that when you mapping reads to the ref genome, you use the parameter: -k 1
hisat2 -x $INDEX --known-splicesite-infile $SPLICE -k 1 --no-unal --summary-file $s.IN.align_summary -p 4 -U $Data/$s.IN.noMyco.fastq.gz |samtools view -bS |samtools sort -o $Output/$s.input.bam
hisat2 -x $INDEX --known-splicesite-infile $SPLICE -k 1 --no-unal --summary-file $s.m6A.align_summary -p 4 -U $Data/$s.m6A.noMyco.fastq.gz | samtools view -bS |samtools sort -o $Output/$s.m6A.bam
However, it could lead to reads mapping to a inappropriate region, because it match k=1.
looking foward your reply
Liangyan
Hi, thanks for your greate workflow for m6A-seq analysis. I noticed you used a randomly sampled 200bp peaks as the background sequence when use Homer to search motifs. I am a bit confused about how to build this background sequence. Would you mind to give the detailed steps?
Thanks a lot.
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