2014-03-20

merge all files in different directories:

find /path/to/directory/ -name *.csv -print0 | xargs -0 -I file cat file > merged.file

samtools view -bS DQB1_030201.sam | samtools sort - DQB1_030201_sorted
samtools index DQB1_030201_sorted.bam DQB1_030201_sorted.bai

samtools view -bS DQB1_030501.sam | samtools sort - DQB1_030501_sorted
samtools index DQB1_030501_sorted.bam DQB1_030501_sorted.bai

samtools view -bS DQB1_0331.sam | samtools sort - DQB1_0331_sorted
samtools index DQB1_0331_sorted.bam DQB1_0331_sorted.bai

samtools view -bS DQB1_040101.sam | samtools sort - DQB1_040101_sorted
samtools index DQB1_040101_sorted.bam DQB1_040101_sorted.bai

samtools view -bS DQB1_040201.sam | samtools sort - DQB1_040201_sorted
samtools index DQB1_040201_sorted.bam DQB1_040201_sorted.bai