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mkdir -p result
cat <<EOF > /dev/null
The options in the command lines below are:
-a : annotation file (GTF by default)
-F : annotation format (GTF by default)
-A : chromosome alias file
-i : input file for reads (SAM by default)
-b : input file is in the BAM format
-o : output file
-p : paired-end assignment
-f : feature-level (exon level) assignment
-O : allowing a read to overlap with multi features
-S : resorting the input SAM or BAM file
-T : threads for assignment
-d and -D : minimum and maximum allowed template lengths
-B : both ends must be mapped in a paired-end fragment
-C : no chimeric fragments are allowed
-M : multi-mapping reads reported by the aligner are allowed
More options are available. Reference to the user guide for the full option list.
EOF
echo
echo "================================================================================"
printf " FeatureCounts Basic Test\n http://subread.sourceforge.net/\n"
echo "================================================================================"
echo
rm -f data/test-minimum.log
# ================================================================================
# The minimum runnable test
../../bin/featureCounts -p -a data/test-minimum.GTF -o result/test-minimum.FC data/test-minimum.sam
echo "================================================================================"
echo "Basic Test finished."
echo "The results are in result/test-minimum.FC"
echo "================================================================================"
echo
echo
echo
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