Possible values are: 
Accent, Accent_r, Blues, Blues_r, BrBG, BrBG_r, BuGn, BuGn_r, BuPu, BuPu_r, 
CMRmap, CMRmap_r, 
Dark2, Dark2_r, 
GnBu, GnBu_r, Greens, Greens_r, Greys, Greys_r, 
OrRd, OrRd_r, Oranges, Oranges_r, 
PRGn, PRGn_r, Paired, Paired_r, Pastel1, Pastel1_r, Pastel2, Pastel2_r, PiYG, PiYG_r, PuBu, PuBuGn, PuBuGn_r, PuBu_r, PuOr, PuOr_r, PuRd, PuRd_r, Purples, Purples_r, 
RdBu, RdBu_r, RdGy, RdGy_r, RdPu, RdPu_r, RdYlBu, RdYlBu_r, RdYlGn, RdYlGn_r, Reds, Reds_r, 
Set1, Set1_r, Set2, Set2_r, Set3, Set3_r, Spectral, Spectral_r, 
Vega10, Vega10_r, Vega20, Vega20_r, Vega20b, Vega20b_r, Vega20c, Vega20c_r, 
Wistia, Wistia_r, YlGn, YlGnBu, YlGnBu_r, YlGn_r, YlOrBr, YlOrBr_r, YlOrRd, YlOrRd_r, 
afmhot, afmhot_r, autumn, autumn_r, 
binary, binary_r, bone, bone_r, brg, brg_r, bwr, bwr_r, 
cool, cool_r, coolwarm, coolwarm_r, copper, copper_r, cubehelix, cubehelix_r, 
flag, flag_r, 
gist_earth, gist_earth_r, gist_gray, gist_gray_r, gist_heat, gist_heat_r, gist_ncar, gist_ncar_r, gist_rainbow, gist_rainbow_r, gist_stern, gist_stern_r, gist_yarg, gist_yarg_r, gnuplot, gnuplot2, gnuplot2_r, gnuplot_r, gray, gray_r, 
hot, hot_r, hsv, hsv_r, 
icefire, icefire_r, inferno, inferno_r, 
jet, jet_r, 
magma, magma_r, mako, mako_r, 
nipy_spectral, nipy_spectral_r, 
ocean, ocean_r, 
pink, pink_r, plasma, plasma_r, prism, prism_r, 
rainbow, rainbow_r, rocket, rocket_r, 
seismic, seismic_r, spectral, spectral_r, spring, spring_r, summer, summer_r, 
tab10, tab10_r, tab20, tab20_r, tab20b, tab20b_r, tab20c, tab20c_r, terrain, terrain_r, 
viridis, viridis_r, vlag, vlag_r, 
winter, winter_r

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