Complexity curve #96
Description
- Looking into complexity curve. Could it be that for PE reads we actually need to add the
-Pparameter in preseq? This was not detected in the pipeline automatically.
samtools sort 6-10A_S13_L001_R1_001_val_1_bismark_bt2_pe.bam \
-m 8589934592 \
-@ 1 \
-o 6-10A_S13_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam
preseq lc_extrap -v -B 6-10A_S13_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam -o 6-10A_S13_L001_R1_001_val_1_bismark_bt2_pe.ccurve.txt
- Also, for very small amounts of the reads this program is not working, but I guess that is my problem with reads of total number 119,573.
Error: max count before zero is less than min required cound (4), sample not sufficiently deep or duplicates removed.
original command:
BAM_INPUT
TOTAL READS = 119573
DISTINCT READS = 119456
DISTINCT COUNTS = 3
MAX COUNT = 3
COUNTS OF 1 = 119342
MAX TERMS = 2
OBSERVED COUNTS (4)
1 119342
2 111
3 3
ERROR: max count before zero is les than min required count (4), sample not sufficiently deep or duplicates removed
and if I implement PE:
PAIRED_END_BAM_INPUT
paired = 119572
unpaired = 0
MERGED PAIRED END READS = 119572
MATES PROCESSED = 239144
TOTAL READS = 119572
DISTINCT READS = 119485
DISTINCT COUNTS = 2
MAX COUNT = 2
COUNTS OF 1 = 119398
MAX TERMS = 2
OBSERVED COUNTS (3)
1 119398
2 87
ERROR: max count before zero is les than min required count (4), sample not sufficiently deep or duplicates removed