ls2017
commented
8 years ago Regarding my question how to prepare input_bam.fofn, my question actually means how to build BAM files?
I found this from the website, which tells 3.0 SMRT is necessary: https://github.com/PacificBiosciences/PacBioFileFormats/wiki/BAM-recipes
When I try to download 3.0 SMRT, it only has preview from the site: http://www.pacb.com/proceedings/pacbio-smrt-analysis-3-0-preview/
When I got to Github, there is only S2.3.0 from https://github.com/PacificBiosciences/SMRT-Analysis
I found all these very confusing.
Could you please explain what software version I actually need to use Falcon output for Falcon_unzip? Say, FalconV0.5 and above, SMRT-analysis 3.0 and the recently released Falcon_unzip?
Then after Falcon, shall I use the original input.fofn listing all the fasta files and the bam files converted by 3.0 SMRT from bax.h5 files to run the unzip.sh and fc_unzip.cfg ?
Could you please advise? I have tried for a couple of weeks and still get nowhere.
Many thanks!
These are the information from https://github.com/PacificBiosciences/PacBioFileFormats/wiki/BAM-recipes This page assumes you have the 3.0 SMRTanalysis stack installed. There is no other supported way to build BAM files according to our requirements. So, for example, if you do not have bax2bam available, there is no other supported way to build a compliant BAM file adhering to our requirements. Building a basecalls BAM file (no alignments) For each run, the PacBio RS gives you three "bax.h5" output files. Use bax2bam to get them into a one BAM file: $ bax2bam m.1.bax.h5 m.2.bax.h5 m.3.bax.h5
peterdfields
xuzhichao830
pb-jchin
I am new to PacBio data analysis and I have just finished a falcon fun and want to use FALCON_unzip to construct haplotype specific contigs/Phased Diploid Genome assembly.
I have installed Falcon_unzip and SMRT-analysis on our HPC.
Under the folder FALCON_unzip-master/examples, there are 2 files: unzip.sh and fc_unzip.cfg
The contents of unzip.sh is as the following: fc_unzip.py fc_unzip.cfg fc_quiver.py fc_unzip.cfg
For cfg file, as our HPC doesn't support SGE, I have adapted the cfg file according to your comments on previous issue #21 ( I can provide my feedback for my running if needed)
[General] job_type = local
[Unzip] input_fofn= input.fofn input_bam_fofn= input_bam.fofn
smrt_bin=/home/peter/bioinformatics/smrtlink/install/smrtlink-fromsrc_3.0.5.175021,175083-175021-174993-174993/bundles/smrttools/smrtcmds/bin/
jobqueue = sge_phasing= sge_quiver= sge_track_reads= sge_blasr_aln= sge_hasm= unzip_concurrent_jobs = 6 quiver_concurrent_jobs = 6
My questions are listed as below:
Question 1: Shall I just run the command: unzip.sh fc_unzip.cfg, which will generate the Phased Diploid Genome assembly at the end?
Question 2: How to prepare input.fofn and input_bam.fofn listed in the cfg file? Does the input.fofn contain the path and names of all the *.bax.h5 files?
Question 3: Since falcon-unzip integrates/calls quiver, is there still any need to run SMRT-analysis alone?
Question 4: I am new to SMRT-analysis, too. Do I need to worry about using the following SMRT commands with settings.xml as mentiond below? If so, where and how to get settings.xml? $ $SMRT_ROOT/current/etc/setup.sh $ smrtpipe.py params=settings.xml xml:input.xml
Question 5: If I don't use Falcon-unzip, what commands from SMRT-analysis people normally use to generate the final assembly from Falcon output? Is it just quiver?
Looking forward to your reply
Many thanks!