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Search: Posts Made By: lingling huang
Forum: Pacific Biosciences 06-01-2017, 11:22 PM
Replies: 2
Views: 3,817
Posted By lingling huang
How to find the corresponding name of isoform name is the gene locus with an index (s

I used the software IDP to analyze iso-seq data. In the final results, I want to extract read sequences according to novel isoforms name from fasta file.
However, I can't find the corresponding...
Forum: Pacific Biosciences 12-20-2016, 12:14 AM
Replies: 0
Views: 1,288
Posted By lingling huang
difference blasr output in two fasta file

Hi There,
Anyone can help me to resolve the problem(shown on screenshot), Why it doesn't work for /gencode.v19.pc_transcripts.fa but does work for /gencode.v19.lncRNA_transcripts.fa?
Anyone used to...
Forum: Pacific Biosciences 10-16-2016, 10:53 PM
Replies: 2
Views: 1,457
Posted By lingling huang
Thank you for response. I known what you mean and...

Thank you for response. I known what you mean and I have tried it before, but it didn't show the same look.
My input file is GFF, is it right?
Forum: Pacific Biosciences 10-16-2016, 06:36 PM
Replies: 2
Views: 1,457
Posted By lingling huang
How to add custom track?

Hi there,
Someone can help me how to add custom track on UCSC like attached picture at below? Thanks a lot!
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Forum: Pacific Biosciences 10-14-2016, 02:59 AM
Replies: 0
Views: 1,155
Posted By lingling huang
Provide sts.csv file

Anyone can provide me with a sts.csv file of good-quality PacBio data? I can't download it from PacBio blog. I want to have a comparative verification.
Thank you!
Forum: Pacific Biosciences 10-14-2016, 01:44 AM
Replies: 2
Views: 1,936
Posted By lingling huang
I missed the live webcast, is there a link i can...

I missed the live webcast, is there a link i can watch the video?
Forum: Pacific Biosciences 10-14-2016, 01:28 AM
Replies: 0
Views: 1,307
Posted By lingling huang
Recommended Loading Percentage of P1 is equivalent to optimal loading?

Hi there,
Does recommended percentage of P1 mean to optimal loading? In my analysis results, the conclusion is not equal.
There pictures are attached below. Any advice would be appreciated!
...
Forum: Pacific Biosciences 09-18-2016, 07:10 AM
Replies: 0
Views: 1,203
Posted By lingling huang
Got the number of mapped gene loci

Hello there,
How to got the correct numbers of mapped gene loci? Due to long transcripts found , there are some isoforms mapped to more than one gene. In such cases, how to got the correct numbers...
Forum: Pacific Biosciences 09-18-2016, 06:58 AM
Replies: 0
Views: 1,147
Posted By lingling huang
nucleus RNA mapped to CHR mitochondria

Hi there,
I got samples from the brain nucleus RNA and sequenced it using PacBio RS2. However, Mitochondria exist only in the cytoplasm,why my data mapped to chrM?(screenshot shown on below) Does my...
Forum: Pacific Biosciences 09-10-2016, 08:33 PM
Replies: 1
Views: 1,515
Posted By lingling huang
Detecting and Visualizing gene fusions

Hi there,
Is the Genomatix Transcriptome Viewer applicable to pacbio transcriptome data for visualization of fusion gene?
Anyone can provide some software for visualizing the PB data? THANK YOU!
Forum: Pacific Biosciences 09-09-2016, 08:18 PM
Replies: 4
Views: 2,006
Posted By lingling huang
Thank you for reply! But there was no reply!

Thank you for reply! But there was no reply!
Forum: Pacific Biosciences 09-07-2016, 07:15 PM
Replies: 4
Views: 2,006
Posted By lingling huang
I have attached screenshot message. Why the...

I have attached screenshot message. Why the result are totally different by using samtools sort and just sort.
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4495

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I look the name of chromosome by using basic Unix commands such...
Forum: Pacific Biosciences 09-07-2016, 05:24 AM
Replies: 4
Views: 2,006
Posted By lingling huang
Error occured in matchAnnot.py

Hi there,
A ERROR occurred during running matchAnnot.py by using human genome hg38 and annotation file v.25. The error message said "chromosome 10 not in annotation" but it actually exist in gtf...
Forum: Pacific Biosciences 09-06-2016, 04:58 AM
Replies: 3
Views: 1,479
Posted By lingling huang
got it! Thank you! But the coverage seems to be...

got it! Thank you! But the coverage seems to be weird(shown below), is it right?

4491
Forum: Pacific Biosciences 09-06-2016, 01:29 AM
Replies: 3
Views: 2,088
Posted By lingling huang
How to filter out all GMAP alignments that have...

How to filter out all GMAP alignments that have less than 90% of the read aligned or less than 80% identity, by using "filterBAM" ?
Forum: Pacific Biosciences 09-05-2016, 07:29 PM
Replies: 3
Views: 1,479
Posted By lingling huang
the quality of Reads of Insert

Hello there,
If the coverage is 30X and the quality of reads of insert is 0.96, is it reasonable? Why do i remenber the accuracy is 0.9999? What the difference between them? Any advice would be...
Forum: Pacific Biosciences 08-30-2016, 05:08 PM
Replies: 2
Views: 1,583
Posted By lingling huang
I see. Thanks a lot.

I see. Thanks a lot.
Forum: Pacific Biosciences 08-29-2016, 11:41 PM
Replies: 2
Views: 1,583
Posted By lingling huang
how to understand the output result of PacBio_BasSummary

Hello there,
I run PacBio_BasSummary.py program, but I can't understand the result. I want to calculate Productivity 0 (%), Productivity 1 (%), Productivity 2 (%) in command-line. Could someone...
Forum: Bioinformatics 08-25-2016, 06:51 PM
Replies: 0
Views: 1,186
Posted By lingling huang
what's the real difference between Gencode v19 and Gencode v24,25 besides the corresp

Hi there,
what's the real difference between Gencode v19 and Gencode v24,25 besides the corresponding usage of different genome verison h19 and h38 ? Such as the numbers and positon of chromosome,...
Forum: Pacific Biosciences 08-19-2016, 02:58 AM
Replies: 0
Views: 1,023
Posted By lingling huang
code for how to extract needed PacBio transcripts

Hi there, I'm new to the bioinformatics and not familiar with programming. I want to filter for transcripts I need, but I don't know how to write code for extracting PacBio transcript that have two...
Forum: Bioinformatics 08-17-2016, 04:48 PM
Replies: 2
Views: 2,494
Posted By lingling huang
Yes, my data are full-length non-chimeric...

Yes, my data are full-length non-chimeric transcripts and have a human reference. Therefore, I want to try to align them to human genome.
Forum: Bioinformatics 08-16-2016, 07:23 PM
Replies: 2
Views: 2,494
Posted By lingling huang
How to find polycistronic transcripts in eukaryotes genomes

Hi,there.
I have got long, high-quality, consensus transcripts sequences, and I want to see weather there are polycistronic transcripts in my PacBia data.I have extracted the long open reading...
Forum: Pacific Biosciences 08-08-2016, 07:49 PM
Replies: 3
Views: 1,376
Posted By lingling huang
tofu_wrap.py --nfl_fa isoseq_nfl.fasta --ccs_fofn...

tofu_wrap.py --nfl_fa isoseq_nfl.fasta --ccs_fofn reads_of_insert.fofn --bas_fofn input.fofn -d clusterOut --quiver --bin_manual "(0,2,4,6,8,9,10,11,12,13,15,17,19,20,23)" --gmap_db...
Forum: Pacific Biosciences 08-08-2016, 07:36 PM
Replies: 15
Views: 3,612
Posted By lingling huang
Thank you for your reply, I've got my problem...

Thank you for your reply, I've got my problem solved and produced final result.
Forum: Pacific Biosciences 08-08-2016, 01:51 AM
Replies: 3
Views: 1,376
Posted By lingling huang
Can use multiple CPUs or thread to speed up the running rate for tofu_wrap.py?

Hi, there. I have 7 smrtcell data. It's really slow to run tofu_wrap.py, I want to know to weather I can use multiple CPUs or thread to speed up the running rate. Thank you for any tips!
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