ambiguous results in .bam file
Closed this issue · 3 comments
Hello dear Felix,
My bismark alignment has finished after 2 days at least ... and I got my report file:
Bismark report for: /home/ubuntu/SRR4298802_1_val_1.fq and /home/ubuntu/SRR4298802_2_val_2.fq (version: v0.24.2)
Bismark was run with Bowtie 2 against the bisulfite genome of /home/ubuntu/ with the specified options: -q --score-min L,0,-0.2 --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)
Final Alignment report
Sequence pairs analysed in total: 171035784
Number of paired-end alignments with a unique best hit: 134138933
Mapping efficiency: 78.4%
Sequence pairs with no alignments under any condition: 24141588
Sequence pairs did not map uniquely: 12755263
Sequence pairs which were discarded because genomic sequence could not be extracted: 65
Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT: 67092253 ((converted) top strand)
GA/CT/CT: 0 (complementary to (converted) top strand)
GA/CT/GA: 0 (complementary to (converted) bottom strand)
CT/GA/GA: 67046615 ((converted) bottom strand)
Number of alignments to (merely theoretical) complementary strands being rejected in total: 0
Final Cytosine Methylation Report
Total number of C's analysed: 4942715100
Total methylated C's in CpG context: 158205936
Total methylated C's in CHG context: 4297893
Total methylated C's in CHH context: 15038457
Total methylated C's in Unknown context: 8857
Total unmethylated C's in CpG context: 54614523
Total unmethylated C's in CHG context: 1027108410
Total unmethylated C's in CHH context: 3683449881
Total unmethylated C's in Unknown context: 1240748
C methylated in CpG context: 74.3%
C methylated in CHG context: 0.4%
C methylated in CHH context: 0.4%
C methylated in Unknown context (CN or CHN): 0.7%
Bismark completed in 1d 21h 5m 45s
but when I want to open the .bam file I see this:
Doc1.docx
why I cant see my bam file??
thanks
I suppose you are now using Samtools to look at the BAM file?
Oops!
I thought bam files are not human-readable
and this is why I can't see the bam file
sorry for my simple question cause I'm so stressed for my work
they are indeed not human readable, but samtools view -h file.bam | head will convert them for you