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I d like to count the reads for each position (keep the information about F or R strand) on my chromosome.
I tried with mpileup but it give me results not easily to manage for a statistical work. Then I tried VarScan..
Reading input from Pileup_merge.pileup (VARSCAN)
chrM 1 G 4 3 G:3:1:21:1:0:3:0
chrM 2 G 4 4 G:4:1:24:1:0:4:0
chrM 3 A 4 4 A:4:1:24:1:0:4:0
chrM 4 T 4 3 T:3:1:23:1:0:3:0
chrM 5 C 2 1 C:1:1:24:1:0:1:0
chrM 6 C 4 3 C:3:1:23:1:0:3:0
mpileup file:
chrM 1 G 4 ^*,^7,^7,^*, 5529
chrM 2 G 4 ,,,, 7;8=
chrM 3 A 4 ,,,, 7:7=
chrM 4 T 4 ,,,, 465=
chrM 5 C 2 ,, 19
chrM 6 C 4 ,,,, 465=
A part that VARSCAN give me error after 300 positions (I ll think after about this error), I don t see the link between these 2 output..
I tried with mpileup but it give me results not easily to manage for a statistical work. Then I tried VarScan..
Reading input from Pileup_merge.pileup (VARSCAN)
chrM 1 G 4 3 G:3:1:21:1:0:3:0
chrM 2 G 4 4 G:4:1:24:1:0:4:0
chrM 3 A 4 4 A:4:1:24:1:0:4:0
chrM 4 T 4 3 T:3:1:23:1:0:3:0
chrM 5 C 2 1 C:1:1:24:1:0:1:0
chrM 6 C 4 3 C:3:1:23:1:0:3:0
mpileup file:
chrM 1 G 4 ^*,^7,^7,^*, 5529
chrM 2 G 4 ,,,, 7;8=
chrM 3 A 4 ,,,, 7:7=
chrM 4 T 4 ,,,, 465=
chrM 5 C 2 ,, 19
chrM 6 C 4 ,,,, 465=
A part that VARSCAN give me error after 300 positions (I ll think after about this error), I don t see the link between these 2 output..