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== unSortBam to Methylfreq (Pair-end)== When you save pair-end reads into one bam file, usually the read1 and read2 would be one by one in the order. However, when you use samtools sort, this order will be changed and therefore, some further analysis would be report error when they require pair-wise order reads, such as bismark_methylation_extractor #!/bin/csh #PBS -N SRR1232311_1_val_1.fq.gz_bismark_bt2_pe.bam #PBS -q glean #PBS -l nodes=1:ppn=6 #PBS -l walltime=6:00:00 #PBS -o SRR1232311_1_val_1.fq.gz_bismark_bt2_pe.bam.log #PBS -e SRR1232311_1_val_1.fq.gz_bismark_bt2_pe.bam.err #PBS -V #PBS -M shihcheng.guo@gmail.com #PBS -m abe #PBS -A k4zhang-group cd /oasis/tscc/scratch/shg047/Xliu2014/bam bismark_methylation_extractor --paired-end --bedGraph --multicore 3 --ignore 3 --ignore_3prime 3 --ignore_r2 5 --ignore_3prime_r2 5 --gzip --buffer_size 4G --zero_based --comprehensive --output ../methyfreq SRR1232311_1_val_1.fq.gz_bismark_bt2_pe.bamrm CHG* CpG* CHH* *bedGraph.gz *bismark.cov.gz Detail Parameters as Following: Parameters used to extract methylation information: Bismark Extractor Version: v0.14.4 Bismark result file: paired-end (SAM format) Ignoring first 3 bp of Read 1 Ignoring first 5 bp of Read 2 Ignoring last 3 bp of Read 1 Ignoring last 5 bp of Read 2 Output specified: comprehensive No overlapping methylation calls specified Collect 0-based Coverage File:
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