Question: What is the next step after download the ncbi sra data of pacbio RSII sequencing
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gravatar for Sparrow_kop
13 months ago by
Sparrow_kop210
China
Sparrow_kop210 wrote:

Hi, guys! I am a newbie in pabio sequence analysis , recently I download some pacbio RSII data from ncbi sra database, after fastq-dump , I get a fastq file which I think is the raw subread data.

But now I want to do ccs(Circular Consensus Sequence calling) step , the pacbio ccs binary software need the bam or bax (bax can be transformed to bam )file as input , also in the sra website , there is no h5 format file submitted by submitter , so there only has fastq file , so I don't know how to do with the pacbio fastq file ? Thanks!

pacbio fastq sra • 1000 views
ADD COMMENTlink modified 13 months ago by harish230 • written 13 months ago by Sparrow_kop210
2
gravatar for harish
13 months ago by
harish230
harish230 wrote:

Since you say that you are getting Fastq/fasta files, the first step is to correct them. The best way to go about it is to either use Falcon till the generation of preads or Canu's correct-trim mode or use proovread.

If you had the bax/bam files, this would have been easier as you could import them into SMRTlink and you could have used it's pushbutton nature :)

ADD COMMENTlink written 13 months ago by harish230

Hi, harish, thanks! I will try it ! Also I had contacted the pacbio support , they said that the best solution is to get the raw bax/bam file......

ADD REPLYlink written 13 months ago by Sparrow_kop210
2
gravatar for lakhujanivijay
13 months ago by
lakhujanivijay4.5k
India
lakhujanivijay4.5k wrote:

Hi Sparrow_kop

I don't know about "pacbio ccs binary software" but you can generate CCS using pabio SMRT link. Take a look at the consensus sequence resulting from alignment between subreads taken from a single ZMW.

SMRT_Technology_SMRTbell_Template

Generation of the CCS read does not include or require alignment against a reference sequence. Generation of CCS reads using the CCS algorithm requires at least two full-pass subreads from the insert

Look at this video

ADD COMMENTlink written 13 months ago by lakhujanivijay4.5k

Hi Vijay Lakhujani , thank you for your answer! I watched the video in your link, but I found that the SMRT link program need the bam/RSII(which is .bax) format file as input ,So it don't support fastq file as input , do you used this program which import fastq file for analysis? thanks!

ADD REPLYlink written 13 months ago by Sparrow_kop210
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