Locate the MethPipe Files

Several files MethPipe-associated files were already provided in the ALPS1 server and they can be found in the /work3/NRPB1219 folder.

ls -lah /work3/NRPB1219/hg18_*

# Console output

-rw-r--r-- 1 s00yao00 s00yao00 1.7M 2014-12-16 15:55 /work3/NRPB1219/hg18_h1_bsseq_methpipe.hmr
-rw-r--r-- 1 s00yao00 s00yao00 777M 2014-12-16 15:55 /work3/NRPB1219/hg18_h1_bsseq_methpipe.meth.corrected
-rw-r--r-- 1 s00yao00 s00yao00 163K 2014-12-16 15:55 /work3/NRPB1219/hg18_h1_bsseq_methpipe.pmd
-rw-r--r-- 1 s00yao00 s00yao00 1.7M 2014-12-17 11:51 /work3/NRPB1219/hg18_h1_hmr.bed
-rw-r--r-- 1 s00yao00 s00yao00 797M 2014-12-16 16:30 /work3/NRPB1219/hg18_h1_meth.bedGraph
-rw-r--r-- 1 s00yao00 s00yao00 169K 2014-12-17 11:51 /work3/NRPB1219/hg18_h1_pmd.bed
-rw-r--r-- 1 s00yao00 s00yao00 2.7M 2014-12-16 15:55 /work3/NRPB1219/hg18_imr90_bsseq_methpipe.hmr
-rw-r--r-- 1 s00yao00 s00yao00 778M 2014-12-16 15:55 /work3/NRPB1219/hg18_imr90_bsseq_methpipe.meth.corrected
-rw-r--r-- 1 s00yao00 s00yao00  83K 2014-12-16 15:55 /work3/NRPB1219/hg18_imr90_bsseq_methpipe.pmd
-rw-r--r-- 1 s00yao00 s00yao00 2.7M 2014-12-17 11:51 /work3/NRPB1219/hg18_imr90_hmr.bed
-rw-r--r-- 1 s00yao00 s00yao00 796M 2014-12-16 16:29 /work3/NRPB1219/hg18_imr90_meth.bedGraph
-rw-r--r-- 1 s00yao00 s00yao00  80K 2014-12-17 11:51 /work3/NRPB1219/hg18_imr90_pmd.bed

For reader who do not have an account on the ALPS server, you may download these files from Dropbox HERE then use gunzip to unpack.

gunzip hg18_*.gz

And you may use awk commands to transform .meth.corrected files into bedGraph format, and .hmr and .pmd files to BED format.

awk -F $'\t' 'BEGIN { OFS=FS } { print $1,$2,$2+1,$5 }' hg18_h1_bsseq_methpipe.meth.corrected > hg18_h1_meth.bedGraph
awk -F $'\t' 'BEGIN { OFS=FS } { print $1,$2,$2+1,$5 }' hg18_imr90_bsseq_methpipe.meth.corrected > hg18_imr90_meth.bedGraph
awk -F $'\t' 'BEGIN { OFS=FS } { density = $5/($3-$2)*1000; print $1,$2,$3,$4,sprintf("%d",density),$6 }' hg18_h1_bsseq_methpipe.hmr > hg18_h1_hmr.bed
awk -F $'\t' 'BEGIN { OFS=FS } { density = $5/($3-$2)*1000; print $1,$2,$3,$4,sprintf("%d",density),$6 }' hg18_imr90_bsseq_methpipe.hmr > hg18_imr90_hmr.bed
awk -F $'\t' 'BEGIN { OFS=FS } { density = $5/($3-$2)*100000; print $1,$2,$3,$4,sprintf("%d",density),$6 }' hg18_h1_bsseq_methpipe.pmd > hg18_h1_pmd.bed
awk -F $'\t' 'BEGIN { OFS=FS } { density = $5/($3-$2)*100000; print $1,$2,$3,$4,sprintf("%d",density),$6 }' hg18_imr90_bsseq_methpipe.pmd > hg18_imr90_pmd.bed