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Forum: Bioinformatics 05-21-2018, 06:57 PM
Replies: 1
Views: 901
Posted By illuminaGA
De novo RNA-Seq Assembly using Trinity with variable length reads

Dear All, i am working on a project that will do De novo RNA-Seq Assembly using Trinity. Totally have 16 samples from 2 projects.

1. 8 sample, PE150, 30x, Hiseq 2500
2. another 8 sample, PE300,...
Forum: Illumina/Solexa 04-19-2018, 05:49 PM
Replies: 0
Views: 769
Posted By illuminaGA
Is it possible to tell if fruit fly eggs belong to its parents by NGS?

Dear All,

I am wondering that if Is it possible to tell if fruit fly eggs belong to its parents by NGS? What is the strategy I can try? NGS or PCR? Any idea will be appreciated. Thanks.

GA
Forum: Bioinformatics 02-09-2018, 04:54 AM
Replies: 11
Views: 2,198
Posted By illuminaGA
Ok, Thanks a lot. Is there an alternative...

Ok, Thanks a lot.

Is there an alternative software for cufflink? It seems very slow.
Forum: Bioinformatics 02-07-2018, 06:48 AM
Replies: 11
Views: 2,198
Posted By illuminaGA
Thanks a lot. I mapped the reads by Tophat, one...

Thanks a lot. I mapped the reads by Tophat, one of the output files is unmapped.bam. Can I just convert this file to a fastq file and map again?

Another sample mapping is still running, I will...
Forum: Bioinformatics 02-05-2018, 06:49 PM
Replies: 11
Views: 2,198
Posted By illuminaGA
Oh no. I will confirm with the lab to see what...

Oh no. I will confirm with the lab to see what kit they use. how should I remove those reads from the raw reads? I saw someone said it's not necessary to do that.

Appreciate your help again.
...
Forum: Bioinformatics 02-05-2018, 06:19 AM
Replies: 11
Views: 2,198
Posted By illuminaGA
Dear GenoMax I just finished the mapping to...

Dear GenoMax

I just finished the mapping to the rRNA reference and got 70% mapping rate. Is this a normal range for the mRNA seq? Can I say 70% reads are rRNA? how to understand the result? Could...
Forum: Bioinformatics 01-23-2018, 10:14 AM
Replies: 11
Views: 2,198
Posted By illuminaGA
Great, Thanks, So what should I do is copy...

Great, Thanks,

So what should I do is copy those sequences into a text file and build as a reference and map the sample sequencing data to this reference, right?

One more question, can I just...
Forum: Bioinformatics 01-18-2018, 06:56 PM
Replies: 11
Views: 2,198
Posted By illuminaGA
Thank you so much. Btw, how / where should I...

Thank you so much.

Btw, how / where should I download the rRNA sequences? I explore the database for hours but still cannot figure out where to download the sequence.

Thanks again.

Al
Forum: Bioinformatics 01-18-2018, 12:19 PM
Replies: 11
Views: 2,198
Posted By illuminaGA
How should I count the percentage of messenger RNA and ribosomal RNA in the samples

Dear All

We have some E coli. total RNA-seq data and my PI would like to count the percentage of messenger RNA and ribosomal RNA in the data. My idea is mapping the data to the transcriptome and...
Forum: Illumina/Solexa 09-07-2017, 07:00 AM
Replies: 58
Views: 40,540
Posted By illuminaGA
Hi Harlon Could you give me some pointers...

Hi Harlon

Could you give me some pointers about how to detect the carryover contamination? Software, pipeline etc. Thank you in advance.
Forum: Bioinformatics 08-29-2017, 12:47 PM
Replies: 1
Views: 755
Posted By illuminaGA
How many reads needed for comparing the genome different bacteria strains.

Dear All

We have a project to identify the different bacteria strains and also want to find the genome different between different strains by WGS method.

The bacteria genome is ~2-3M.

So how...
Forum: Bioinformatics 08-23-2017, 08:16 AM
Replies: 6
Views: 1,287
Posted By illuminaGA
That great information, Thank you so much

That great information, Thank you so much
Forum: Bioinformatics 08-22-2017, 11:18 AM
Replies: 6
Views: 1,287
Posted By illuminaGA
Thank you so much. Let me digest the paper.

Thank you so much. Let me digest the paper.
Forum: Bioinformatics 08-21-2017, 11:45 AM
Replies: 6
Views: 1,287
Posted By illuminaGA
Thanks. I will try. Yes, I was thinking...

Thanks. I will try.

Yes, I was thinking about assembly the transcripts first based on the reference-free strategies.
Forum: Bioinformatics 08-21-2017, 09:30 AM
Replies: 6
Views: 1,287
Posted By illuminaGA
Can I use E. coli K strains reference for B strains Differential Gene Exp analysis?

Dear All, I currently have a project for E. coli B strains Differential Gene Exp analysis. I did some search only found genome ref for K strains. So I am wondering Can I use E. coli K strains...
Forum: Bioinformatics 07-18-2017, 05:42 AM
Replies: 0
Views: 598
Posted By illuminaGA
Pipeline for identification of CRISPR/Cas9-induced indel?

Dear All

We have a new project about the identification of CRISPR/Cas9-induced indels.
Is there any stable pipeline for this analysis? I checked some literature, it seems everyone uses different...
Forum: Bioinformatics 06-26-2017, 07:11 AM
Replies: 3
Views: 1,777
Posted By illuminaGA
Thank you so much. Is the mothur the best...

Thank you so much.

Is the mothur the best pipeline currently?
Forum: Bioinformatics 06-23-2017, 05:56 AM
Replies: 3
Views: 1,777
Posted By illuminaGA
Qiime vs illumina basespace 16s pipeline, Which is better?

Hello everyone, we currently handle a 16 project which analyzed by QIime and illumina basespace 16s app. The results are quite different. I googled and didn't find any information about comparing...
Forum: Illumina/Solexa 05-19-2017, 10:01 AM
Replies: 5
Views: 1,154
Posted By illuminaGA
Thank you.

Thank you.
Forum: Illumina/Solexa 05-19-2017, 09:04 AM
Replies: 5
Views: 1,154
Posted By illuminaGA
Help!, strange fastq format

Dear All

I download some fastq reads from SRA, but the format is wired. The reads are all number and dots.
Please give me some pointers if you have seen this before? Thank you in advance.
...
Forum: RNA Sequencing 05-02-2017, 08:23 AM
Replies: 3
Views: 2,151
Posted By illuminaGA
Sorry if this is a dumb question. How should...

Sorry if this is a dumb question.

How should I choose the GFT file for small RNA seq analysis? Can I use the same gene annotation GFT for regular RNA-seq pipeline? Thank you in advance.
Forum: Bioinformatics 05-02-2017, 08:16 AM
Replies: 5
Views: 4,297
Posted By illuminaGA
Sorry if this is a dumb question. How should...

Sorry if this is a dumb question.

How should I choose the GFT file for small RNA seq analysis? Can I use the same gene annotation GFT for regular RNA-seq pipeline? Thank you in advance.
Forum: Bioinformatics 07-26-2016, 08:43 AM
Replies: 1
Views: 1,205
Posted By illuminaGA
What is the most popular and best tools/pipeline for small RNA seq analysis?

Dear All

I have to analyze a small RNA-seq data. This is my first time working with small RNA. I search threads here but the most recent is 2013.There are several new tools since 2015 but they...
Forum: Bioinformatics 02-04-2016, 01:01 PM
Replies: 0
Views: 1,028
Posted By illuminaGA
Can not pass QC when imputate wiith Michigan Imputation Serve and HRC reference

Hello All.

I have 88 samples in 23andme format. The population is EUR. And I would like to do imputation with Michigan Imputation Serve and Haplotype Reference Consortium panels.

The first...
Forum: Bioinformatics 12-16-2015, 12:31 PM
Replies: 1
Views: 1,228
Posted By illuminaGA
SNP call by samtools, but ALT is "X" QUAL is "0"

Dear All

I had an issue when I did SNP calling by samtools 1.1 with the following commend " samtools mpileup -f hg18chr.fa -u -v 1.bam 2.bam 3.bam 4.bam 5.bam 6.bam 7.bam 8.bam 9.bam -o output.vcf...
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