Example: Mapping¶

---

Example: BAT_mapping ¶

(USAGE: BAT_mapping)

Command¶

BAT_mapping -g genomes/hg19/hg19_chr19.fa -q raw/S5.1_R1.fastq.gz -p raw/S5.1_R2.fastq.gz -i genomes/hg19/hg19_chr19 -o mapped/S5.1 -t 4

Output files¶

mapped/S5.1.bam
mapped/S5.1.bam.bai
mapped/S5.1.excluded.bam
mapped/S5.1.excluded.bam.bai
mapped/S5.1.unmapped.gz
mapped/S5.1.mapping.log

View¶

$ samtools view -h mapped/S5.1.bam | head -4
@HD     VN:1.0  SO:coordinate
@SQ     SN:chr19        LN:59128983
@PG     ID:segemehl     VN:0.2.0-$Rev: 420 $ ($Date: 2015-10-27 19:51:48 +0100 (Tue, 27 Oct 2015) $)    CL:segemehl -s -d genomes/hg19/hg19_chr19.fa -i genomes/hg19/hg19_chr19.ctidx -j genomes/hg19/hg19_chr19.gaidx -F 1 -t 4 -q raw/S5.1_R1.fastq.gz -u mapped/S5.1.unmapped -o mapped/S5.1.sam -p raw/S5.1_R2.fastq.gz
HWI-ST509:187:C130GACXX:1:2105:7981:95727 2:N:0:        153     chr19   117927  255     101M    *       0       0       CAAGGTTATAGTAATTAAAACAGTATGGTACTGGTATTAAAATAGAGATATAGATCAATGGAATAGAACAGAGCTTTTAGAAATAATGTCGCATATTTATA   CECCC>CD@DBDFEHHHHHDIHGIHIEIHFBIHHHHHDJJJIIIGHGIIIJIJIHIJJJJGJIGJIIHIIJIJJJJJJJGJJIFIHGGDHHGHFFFFFCCC   NM:i:0  MD:Z:101        NH:i:15 XI:i:8  XA:Z:M  XB:Z:F1/CT      XD:i:15 XF:i:0

(top)

---

Example: BAT_mapping_stat ¶

(USAGE: BAT_mapping_stat)

Command¶

BAT_mapping_stat --bam mapped/S5.1.bam --excluded mapped/S5.1.excluded.bam --fastq raw/S5.1_R1.fastq.gz >mapped/S5.1.stat

Output file¶

mapped/S5.1.stat
mapped/S5.1.pdf

View¶

$ head -18 mapped/S5.1.stat
-----------mapped/S5.1.bam-----------
-----------------------------
--------   SUMMARY   --------
-----------------------------
total amount of MAPPINGS:       125655
total amount of query READS:    60844

MAPPED READS:
unique paired end:      58778 (96.77%)
multiple paired end:    666 (1.13%)
unique one mate:        753 (1.24%)
multiple one mate:      242 (0.4%)
unique single end:      0 (0%)
multiple single end:    0 (0%)
sum of mapped reads:    60557 (99.53%)
sum of mapped mates:    120119

-----------------------------

(top)

---

Example: BAT_merging ¶

(USAGE: BAT_merging)

Command¶

BAT_merging -o mapped/S5.bam --bam mapped/S5.1.bam,mapped/S5.2.bam

Output files¶

mapped/S5.bam
mapped/S5.bam.bai

View¶

samtools view mapped/S5.bam | head -2
HWI-ST509:187:C130GACXX:1:2105:7981:95727 2:N:0:        153     chr19   117927  255     101M    *       0       0       CAAGGTTATAGTAATTAAAACAGTATGGTACTGGTATTAAAATAGAGATATAGATCAATGGAATAGAACAGAGCTTTTAGAAATAATGTCGCATATTTATA   CECCC>CD@DBDFEHHHHHDIHGIHIEIHFBIHHHHHDJJJIIIGHGIIIJIJIHIJJJJGJIGJIIHIIJIJJJJJJJGJJIFIHGGDHHGHFFFFFCCC   NM:i:0  MD:Z:101        NH:i:15 XI:i:8  XA:Z:M  XB:Z:F1/CT      XD:i:15 XF:i:0  RG:Z:S5.1
HWI-ST952:110:D1BPMACXX:2:1106:2527:83172 2:N:0:        163     chr19   163245  255     1M1I28M =       163347  72      TATTTTTTTTTTTTTTTTTTTTTTTTTAAA  C@@FFFFFHHHHHIJJIHFDDDDDDD-2>A  NM:i:1  MD:Z:29 NH:i:27XI:i:26  XA:Z:P  XB:Z:F1/GA      XD:i:2  XF:i:0  RG:Z:S5.2

---

(top)