Hi all,
I am aligning pacbio reads to a reference genome using gmap. Do you know how to output an extended CIGAR in output sam file from...
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extended cigar in gmap
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extended cigar in bwa-mem
Hi all,
I am aligning pacbio reads to a reference genome using bwa mem. Do you know how to output an extended CIGAR in output sam file... -
Pacbio assembly of polymorphic genome
Hi guys,
a quick question. I am new to pacbio. I've just received pacbio data for assembling a genome (low coverage). It comes from a highly... -
unique isoform detection using IsoSeq
Hi all,
I launched Iso-Seq on my RNA data (D. melanogaster). My aim is to see how many isoforms per gene are there in my sample. I am... -
how can I get abundance from both Iso-seq output and illumina data?
Hi,
We've got the done the RNA-seq of a species (genome is about 3GB), but NO reference genome is available, using pacbio and Illumina. After the... -
Low read counts from old PacBio data
I've been helping other people with processing PacBio data using the SMRTanalysis software. Basically, for our purposes, I've just been using the reads...Last edited by anjama; 09-20-2016, 08:34 AM. -
Circular contig in multicontig reference remapping (SMRTPipe, BLASR)
Hello everybody,
I am doing a secondary analysis involving temporal data (IPDs) using SMRTPipe. I am using P_Mapping (BLASR) to map reads... -
Why the pacbio isoseq data used for RNA analysis is much more than illumina data?
As we all know, for the human RNA-seq analysis, 4-6G clean data from illumina platform is enough. But when I use pacbio's ISO-seq pipline, the subread... -
CANU-correct subreads individually VS batch
When my Pacbio sequencing was done I ended up with 18 subreads that each contained xxxx number of sequences (6,431,149 sequences in total for all 18 subreads).... -
Does the Mixed samples effects the IsoSeq Analysis?
Hi, pacbio
Recently we got the mixed wheat samples with different treatment and used the SMRT(Pacific Biosciences) sequencing system PacBio RS II...Last edited by huan; 06-02-2016, 02:58 AM. -
Keep quality score when correcting with Canu assembler?
I am using Canu assembler to do a de novo assembly of PacBio data. I noticed that when I corrected my reads it produced a .fasta not a .fastq file, therefore... -
Canu error: 'failed to create the overlap store'
Trying to run the following command:
$ canu -trim -p PacBio10_trimmed -d PacBio10_trimmed genomeSize=200000 -pacbio-corrected /work/03868/lguzmanz/liz_trials/PacBio_correctedreads/corrected_Canu_pacbio10.correctedReads.fasta.gz... -
Combined assembly analysis (short reads + long reads)
Dear NGS Experts,
I have a question about combined genome assembly.
We have 75X Hiseq sequencing of an animal species genome... -
How much of PacBio ZMW Loading Productivity 1（p1） is best for IsoSeq?
Hi,
Now I am investigateing the IsoSeq in PacBio platform. I find that the ZMW Loading Productivity 1(P1) varies a lot from different experiments.... -
Genome assembly Using Celera Assembler with corrected data from LoRDEC
Hi,
I corrected PacBio reads Using LoRDEC tool , now I have a corrected fasta file.
My question,
Can I use Celera Assembler with...
