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host_map counts unmapped only if both mates unmapped #291

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host_map counts unmapped only if both mates unmapped #291

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host_map counts unmapped only if both mates unmapped
averagehat Apr 6, 2016
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averagehat Apr 7, 2016
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13 changes: 10 additions & 3 deletions pathdiscov/host_map/bwa_filter_host.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ db=$5 # database
paired=$6 # paired - 1 if paired data, 0 if not
wellpaired=$7 # wellpaired - 1 if paired data "well-paired" (i.e., mate files have exact same IDs), 0 if not
opts=$8 # options

droppair=1
if ! cd ${outputdir}; then

echo "[error] changing directories";
Expand Down Expand Up @@ -46,10 +46,17 @@ else

echo "[stats] paired stats"
samtools flagstat paired.bam

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Can you add a comment above each of the commands
# Extracts unmapped read names as well as their mate
# Extracts unmapped reads, leaving unpaired mates

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done

if [ "$droppair" == 1 ]; then
samtools view paired.bam -f 12 | cut -f1 | sort -u | awk '{print "@"$0}' > paired.unmap.id
else
#could maybe use samtools view paired.bam -f 4 . . . instead
cat paired.sam | awk '$3=="*"' | cut -f1 | sort -u | awk '{print "@"$0}' > paired.unmap.id
fi


# get unmapped read IDs
cat paired.sam | awk '$3=="*"' | cut -f1 | sort -u | awk '{print "@"$0}' > paired.unmap.id
rm paired.sam
# get unmapped read IDs

# extract the 4 line chunks from a fastq file, given in argument 1 file, for IDs give in argument 2 file
cmd="fastq_extract_id.pl ${r1} paired.unmap.id > R1.unmap.fastq"
Expand Down