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process_scripts
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ff48f141
Commit
ff48f141
authored
1 year ago
by
Peng Lian
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Bugfix in rnasequalign.sh
parent
7c9cb1b2
Branches
master
Tags
version_1.1.6
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alignment/rnaseqalign.sh
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alignment/rnaseqalign.sh
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ff48f141
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@@ -91,7 +91,7 @@ fi
idx
=
"
${
index_path
}
/genome"
if
[[
-d
${
index_path
}
/hisat_index
]]
then
idx
=
"
${
index_path
}
/hisat_index/genome"
idx
=
"
${
index_path
}
/hisat_index/genome"
fi
hisat2
-p
$NPROC
--rg-id
${
pair_id
}
--rg
LB:tx
--rg
PL:illumina
--rg
PU:barcode
--rg
SM:
${
pair_id
}
--dta
-x
${
idx
}
$hisat_opt
-S
out.sam
--summary-file
${
pair_id
}
.alignerout.txt
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