Update bamtobigwig.sh

Danko-Lab · Jan 15, 2019 · f5bf5d0 · f5bf5d0
1 parent b598fe9
commit f5bf5d0
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/dnase/BamToBigWig/bamtobigwig.sh b/dnase/BamToBigWig/bamtobigwig.sh
@@ -223,7 +223,7 @@ if [[ "$SEQ" == "SE" ]] ; then
    bedtools genomecov -bg -i  ${TMPDIR}/$j.bed.gz -g ${CHINFO} -strand - > ${TMPDIR}/$j\_minus.noinv.bedGraph
 
 
-   ## Invert minus strand and shift reads.
+   ## Invert minus strand.
    cat ${TMPDIR}/$j\_minus.noinv.bedGraph | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4}' > ${TMPDIR}/$j\_minus.bedGraph 
 
    ## Then to bigWig
@@ -249,7 +249,7 @@ elif [[ "$SEQ" == "PE" ]] ; then
    bedtools genomecov -bg -i  ${TMPDIR}/$j.bed.gz -g ${CHINFO} -strand - > ${TMPDIR}/$j\_minus.noinv.bedGraph
 
 
-   ## Invert minus strand and shift reads.
+   ## Invert minus strand.
    cat ${TMPDIR}/$j\_minus.noinv.bedGraph | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4}' > ${TMPDIR}/$j\_minus.bedGraph 
 
    ## Then to bigWig