Question: Pacbio SRA data format error
0
gravatar for shounak.chakraborty1990
7 days ago by

Hi Everyone,

I am trying to replicate the results of the following paper: https://genome.cshlp.org/content/28/3/396

The data is long reads from Pacbio RS II and is available in SRA in the following location : https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SAMN06328616&o=acc_s%3Aa

I am getting an error "ERROR, could not read quality metrics for FASTQ Sequence" when I try to use the program bax2bam to convert the legacy pacbio files to pacbio bam files.

Any suggestions how to convert the files from SRA to pacbio bam files to be used with the IsoSeq3 pipeline?

Thanks

isoseq3 pacbio sra bax2bam • 64 views
ADD COMMENTlink written 7 days ago by shounak.chakraborty19900

Are you using the original data files found under the Data Access tab of a the samples? A representative example from your data here. If not, try those bax files.

ADD REPLYlink written 7 days ago by GenoMax96k

Yes I am trying out the bax files from the Data Access tab. Here is an example file name.

m140326_081232_42154_c100620072550000001823110407181433_s1_p0.1.bax.h5.1

As I mentioned I got the error with these bax files. I have also tried to remove the .1 after the .h5 but still getting the same error. "ERROR, could not read quality metrics for FASTQ Sequence"

ADD REPLYlink written 7 days ago by shounak.chakraborty19900

Have you tried multiple files and do they all get the same error?

ADD REPLYlink written 7 days ago by GenoMax96k

I am getting the error for multiple files.

ADD REPLYlink written 7 days ago by shounak.chakraborty19900
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