Alignment

CMD go through

bowtie2  -X2000 --mm --local -1 $fastq1 -2 $fastq2 | samtools view -Su /dev/stdin | samtools sort & index > xxx.PE2SE.bam &.bai 2> align.log

For bowtie2:

• Use memory-mapped I/O to load the index (--mm);
• '-X2000' means maximum fragment length for valid paired-end alignments is 2000bp;
• --local: a preset options mode, default as --sensitive-local,

For samtools view:

• -S: ignore for compatibility with previous samtools versions
• -u: uncompressed BAM outputs

SE

bowtie2    --local -x $bowtie2_idx  --threads 8 -U /home/zhc268/scratch/seqdata/EC9.fastq.bz2 2> ${align.log} | \
    samtools view -Su /dev/stdin | samtools sort - $prefix

NOTE on paired-end alignments

• Currently the name tag including PE2SE; it probably is a wrong indicator as we didn't convert PE to SE.