The PacBio BAM specification version described here is 3.0.4. PacBio BAM files adhering to this spec contain the tagpb:3.0.4in the@HDheader. Coordinate conventions The BAM format uses a 0-based coordinate system to refer to positions and intervals on the reference. ...
This library isnotintended to be used as a general-purpose BAM utility - all input & output BAMs must adhere to thePacBio BAM format specification. Non-PacBio BAMs will cause exceptions to be thrown. Documentation FAQ pbbamvalidates all BAM files, and as part of this validation, it checks...
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By sequencing and analysis, a total of 14,776,542 subreads (46 Gb of bam file) were obtained. A total of 236,267 isoforms were obtained, comprising 36,824 HQ transcripts and 199,443 LQ transcripts. On the other hand, a total of 6,574 LncRNAs were predicted based on SMRT sequencing....
Next, create two "files-of-file-names", ("fofn") for the PacBio subread data in fasta and bam format. You need thesubreads.fastafor FALCON and FALCON-Unzip and thesubreads.bamfor the polishing step of FALCON-Unzip. $ cat subreads.fasta.fofn /path/to/my/data/dir/F1_bull_test.sub...
$ /data1/chenying/bs3/hifimeth/src/scripts/hifimeth.sh \ --src /data1/chenying/bs3/hifimeth \ --num_threads 48 \ --model_path /data1/chenying/bs3/hifimeth/models/hifimeth-mol-k400.ckpt \ --input /data1/chenying/bs3/hifimeth/examples/chr1-reads.bam \ --out 5mc-call Resul...
PacBio BAM C++ library. Contribute to PacificBiosciences/pbbam development by creating an account on GitHub.