samtools view -h hur_MO-h6_rep2.sorted.bam NM_001002366 > test.sam

# convert bam directly
samtools view -bS HG00096.chr20.sam > HG00096.chr20.bam

# specific multiple chromosome or regions by space
samtools view -bS *bam chr1 chr2 chr3 > test.bam

# number of entries excluding those marked as read #1 in a pair
[zhangqf7@bnode02 decay]$ samtools view -F 0x40 RIP_h4.bam| cut -f1 | sort | uniq | wc -l
104336

[zhangqf7@bnode02 decay]$ samtools flagstat RIP_h4.bam
208877 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
208877 + 0 mapped (100.00% : N/A)
208877 + 0 paired in sequencing
104541 + 0 read1
104336 + 0 read2
200984 + 0 properly paired (96.22% : N/A)
207883 + 0 with itself and mate mapped
994 + 0 singletons (0.48% : N/A)
71 + 0 with mate mapped to a different chr
71 + 0 with mate mapped to a different chr (mapQ>=5)

# Count mapped reads number from sam file
[zhangqf7@ZIO01 bowtie2_genome]$ samtools flagstat riboseq.sam
1704656 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
1704656 + 0 mapped (100.00% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

# for single-end data
[zhangqf7@bnode02 decay]$ samtools view -F 0x904 RIP_h4.bam| cut -f1 | sort | uniq | wc -l
104971

# for pair-end data
[zhangqf7@bnode02 decay]$ samtools view -F 0x4 RIP_h4.bam| cut -f1 | sort | uniq | wc -l
104971

# old version
bamCoverage --bam RIP_h6.bam --outFileName RIP_h6.bam.bw --binSize 1 --normalizeTo1x 37421801
# 37421801, the total bases in our merge reference

# new version of bamCoverage (DeepTools)
bamCoverage --bam RIP_h6.bam --outFileName RIP_h6.bam.bw --binSize 1 --effectiveGenomeSize 37421801 --normalizeUsing RPGC

# RPGC: RPGC (per bin) = number of reads per bin / scaling factor for 1x average coverage. This scaling factor, in turn, is determined from the sequencing depth: (total number of mapped reads * fragment length) / effective genome size. The scaling factor used is the inverse of the sequencing depth computed for the sample to match the 1x coverage. This option requires –effectiveGenomeSize. 

igvtools count -w 1 RIP_h4.bam RIP_h4.wig /Share/home/zhangqf7/gongjing/zebrafish/data/reference/gtf/refseq_ensembl91_merge.tarns.fa