spike notes

/data/data/bowtie2-2.3.5.1-linux-x86_64/bowtie2-build /data/data/spike.fa spike
#sumest i viena folderi spike paskui ir
export BOWTIE2_INDEXES=/data/data_fastq/reads_colapsed/spike/
for file in *.fa; do /data/data/bowtie2-2.3.5.1-linux-x86_64/bowtie2 -f -N 0 --no-unal -x spike -U $file -S ${file%fa}sam; done
for file in *.sam; do grep -v "@" $file | awk -F "\t|x" '{print $4, " ", $2}' | sort -k 1 > ${file}.out; done
# tmp yra visur po 0 dar, kad susivienodintu eiluciu sk
for file in *.out; do cat tmp >> $file; done
for file in *.out; do cat $file | awk '{ seen[$1] += $2 } END { for (i in seen) print i, seen[i] }' | sort -k 1 > ${file}.out; done
pirmas stulpelis tai tmp su nauje eilute
for file in ../fastq/*/; do var=$(echo $file | cut -d '/' -f 3) && echo $var > $var; done
for file in ../fastq/*/; do var=$(echo $file | cut -d '/' -f 3) && awk '{print $2}' ${var}_reads_colapsed.sam.out.out >> $var; done
paste -d "," tmp ???? > composition_matrix_spike.csv