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Forum: Pacific Biosciences 08-01-2016, 06:57 AM
Replies: 10
Views: 1,611
Posted By bowhan
The error message indicates a (solved) issue...

The error message indicates a (solved) issue described here:
https://github.com/PacificBiosciences/cDNA_primer/issues/3
Please try the method described in this thread. If the error remains,...
Forum: Pacific Biosciences 07-29-2016, 10:42 AM
Replies: 10
Views: 1,611
Posted By bowhan
To me this is a different error from the one...

To me this is a different error from the one described originally.

This one is on DALIGNER itself. The version shipped within ToFU is pretty outdated. Several bugs have been found and fixed since...
Forum: Pacific Biosciences 07-28-2016, 09:07 AM
Replies: 10
Views: 1,611
Posted By bowhan
Looks like the issue described here: ...

Looks like the issue described here:
http://seqanswers.com/forums/showthread.php?t=67094

Can you please attach your "reads_of_insert.fofn" and "input.fofn" files?
Forum: Pacific Biosciences 07-05-2016, 08:23 AM
Replies: 15
Views: 2,515
Posted By bowhan
It clearly had a different error now, which said...

It clearly had a different error now, which said that you didn't have pysam.
Were you following the instruction here...
Forum: Pacific Biosciences 06-29-2016, 07:46 PM
Replies: 15
Views: 2,515
Posted By bowhan
You seems to have one `bax.h5` missing and one...

You seems to have one `bax.h5` missing and one `bas.h5` there. Can you please fix that and try again?
You should already see the duplication after `CircularConsensus` run (no need to run...
Forum: Pacific Biosciences 06-29-2016, 07:28 PM
Replies: 15
Views: 2,515
Posted By bowhan
The awk command parses the input file line by...

The awk command parses the input file line by line, counting how many times each header appears. At last, it prints out all the headers (with their times of appearances) if it appears more than once....
Forum: Pacific Biosciences 06-29-2016, 07:14 PM
Replies: 15
Views: 2,515
Posted By bowhan
can you please check how many of them are...

can you please check how many of them are duplicated? perhaps with

awk '/>/{++a[$1]}END{for(b in a) if(a[b]>1) printf "%s\t%d\n", b, a[b]}' isoseq_flnc.fa


Thanks
Forum: Pacific Biosciences 06-29-2016, 06:41 PM
Replies: 15
Views: 2,515
Posted By bowhan
The job failed because the system call on the...

The job failed because the system call on the `blasr` command failed.
It actually gave an error message complaining that "m151230.../29032/536_60_CCS" is not unique. This is weird if you didn't...
Forum: Pacific Biosciences 06-27-2016, 11:33 AM
Replies: 1
Views: 1,109
Posted By bowhan
pacBio has less # of reads than illumina does,...

pacBio has less # of reads than illumina does, but each read is much longer.
And barcoding is more common on illumina platforms. Based on your number (4-6G), you are probably talking about barcoded...
Forum: Pacific Biosciences 06-27-2016, 11:18 AM
Replies: 15
Views: 2,515
Posted By bowhan
can you please paste the log? and the content of...

can you please paste the log? and the content of the output directory (the output of `tree` command for example).
Forum: Pacific Biosciences 06-23-2016, 09:44 AM
Replies: 4
Views: 1,697
Posted By bowhan
the "combined" means to combine output from...

the "combined" means to combine output from different size bins (it is recommended to sequence cDNAs in different sizes separately to avoid loading bias).
In ToFU, you can and probably should use...
Forum: Pacific Biosciences 06-03-2016, 04:12 AM
Replies: 12
Views: 2,287
Posted By bowhan
"g_consensus.fasta" is a output generated by a...

"g_consensus.fasta" is a output generated by a test script. Its absence suggests the failure of the test job, mostly due to SGE settings.

Were you running tofu under `smrtshell`? If so, it is...
Forum: Pacific Biosciences 06-02-2016, 11:12 AM
Replies: 1
Views: 994
Posted By bowhan
I have not seen a wheat sample before but I don't...

I have not seen a wheat sample before but I don't think mixing samples in general has an impact on this.

Is the mixed sample barcoded?
If they are, can you split them and run them individually?...
Forum: Pacific Biosciences 03-28-2016, 06:24 PM
Replies: 8
Views: 2,250
Posted By bowhan
Thanks for the update. Please be sure to...

Thanks for the update.
Please be sure to include the full path of the file, with probably `ls -1 $PWD/*bax.h5` or `ls *bax.h5 | xargs readlink -f`.
Forum: Pacific Biosciences 03-28-2016, 10:38 AM
Replies: 8
Views: 2,250
Posted By bowhan
smrtshell erases your own environmental variables...

smrtshell erases your own environmental variables and loads only the ones related to smrtanalysis, thus ensures the correct scripts been called. It's located in the smrtanalysis directory, under the...
Forum: Pacific Biosciences 03-25-2016, 05:22 AM
Replies: 8
Views: 2,250
Posted By bowhan
Are all of your scripts from smrtanalysis? Have...

Are all of your scripts from smrtanalysis? Have you manually installed any components from github? Did you invoke `smrtshell` before running anything?

If you want to manually re-run alignment +...
Forum: Pacific Biosciences 03-24-2016, 05:11 AM
Replies: 8
Views: 2,250
Posted By bowhan
Yes 13: Correct 4: Since you don't...

Yes


13: Correct
4: Since you don't have a genome, tofu won't be able to remove redundant transcripts since it does so using the genomic coordinates. You can use other tools like CD-HIT...
Forum: Pacific Biosciences 01-04-2016, 07:02 AM
Replies: 1
Views: 808
Posted By bowhan
The following paper has proposed splicing graph...

The following paper has proposed splicing graph to detect splicing isoforms using EST without a reference genome:

Heber, S., Alekseyev, M., Sze, S. H., Tang, H. & Pevzner, P. A. Splicing graphs...
Forum: Pacific Biosciences 12-23-2015, 08:42 PM
Replies: 3
Views: 1,940
Posted By bowhan
The following is the part of the code dbg2olc...

The following is the part of the code dbg2olc uses to parse the option 'f':


if (strcmp(argv[i], "f") == 0)
{
i++;
LongReadFilenameVec.push_back(argv[i]);
string name1= argv[i];...
Forum: Pacific Biosciences 12-22-2015, 02:55 AM
Replies: 5
Views: 2,094
Posted By bowhan
I am not aware of any PacBio/illumina hybrid...

I am not aware of any PacBio/illumina hybrid transcriptome assembler.

A CAGE library would be the most accurate method to determine the 5' ends/TSS. I would recommend GRIT...
Forum: Pacific Biosciences 12-02-2015, 10:17 AM
Replies: 3
Views: 1,582
Posted By bowhan
You can basically treat the Iso-Seq output as an...

You can basically treat the Iso-Seq output as an assembled transcriptome using second generation sequencing, or EST using sanger.
So tools like transdecoder (https://transdecoder.github.io/),...
Forum: Pacific Biosciences 12-02-2015, 10:08 AM
Replies: 5
Views: 2,094
Posted By bowhan
The lost of 5' end sequence could be due to the...

The lost of 5' end sequence could be due to the degradation of the RNA sample, since the current protocol does not enforce an intact 5' end. There are methods to enrich intact RNA with 5' cap, for...
Forum: Pacific Biosciences 10-27-2015, 08:36 AM
Replies: 12
Views: 2,287
Posted By bowhan
Seems that the node running daligner has...

Seems that the node running daligner has incompatible shared libraries from the node compiling it (probably not all of your nodes have the same versions of OS).

The easiest solution in my opinion...
Forum: Bioinformatics 10-21-2015, 01:48 PM
Replies: 2
Views: 1,109
Posted By bowhan
1. with --bamRemoveDuplicatesType...

1. with --bamRemoveDuplicatesType UniqueIdentical, STAR does not "remove" the duplicates from the bam, but mask them as PCR duplicates by turning on a bit in the bitflag field. If you do `samtools...
Forum: Pacific Biosciences 10-21-2015, 09:56 AM
Replies: 3
Views: 1,262
Posted By bowhan
Like `bash` command itself, when you directly...

Like `bash` command itself, when you directly call "smrtshell" it creates an interactive shell and breaks your flow. But if you gives it a script as an option, it will execute it and return to the...
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