4 OUTSIDER
OUTSIDER are TE no assembled on genome
4.1 MAPPING
Information samtools stats
File : OUTSIDER/MAPPING/stats.txt
## [1] "raw total sequences: 418"
## [2] "filtered sequences: 0"
## [3] "sequences: 418"
## [4] "is sorted: 0"
## [5] "1st fragments: 418"
## [6] "last fragments: 0"
## [7] "reads mapped: 362"
## [8] "reads mapped and paired: 0 # paired-end technology bit set + both mates mapped"
## [9] "reads unmapped: 56"
## [10] "reads properly paired: 0 # proper-pair bit set"
## [11] "reads paired: 0 # paired-end technology bit set"
## [12] "reads duplicated: 0 # PCR or optical duplicate bit set"
## [13] "reads MQ0: 4 # mapped and MQ=0"
## [14] "reads QC failed: 0"
## [15] "non-primary alignments: 677"
## [16] "total length: 10574910 # ignores clipping"
## [17] "total first fragment length: 10574910 # ignores clipping"
## [18] "total last fragment length: 0 # ignores clipping"
## [19] "bases mapped: 9145986 # ignores clipping"
## [20] "bases mapped (cigar): 7883228 # more accurate"
## [21] "bases trimmed: 0"
## [22] "bases duplicated: 0"
## [23] "mismatches: 3052393 # from NM fields"
## [24] "error rate: 3.872009e-01 # mismatches / bases mapped (cigar)"
## [25] "average length: 25298"
## [26] "average first fragment length: 25299"
## [27] "average last fragment length: 0"
## [28] "maximum length: 118886"
## [29] "maximum first fragment length: 0"
## [30] "maximum last fragment length: 0"
## [31] "average quality: 21.9"
## [32] "insert size average: 0.0"
## [33] "insert size standard deviation: 0.0"
## [34] "inward oriented pairs: 0"
## [35] "outward oriented pairs: 0"
## [36] "pairs with other orientation: 0"
## [37] "pairs on different chromosomes: 0"
## [38] "percentage of properly paired reads (%): 0.0"4.2 SV ANALYSIS
Informations of SV.vcf file.
## grep: ../../OUTSIDER/TrEMOLO_SV_TE/HARD/HARD.fasta: No such file or directory