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Forum: The Pipeline 02-16-2017, 12:26 PM
Replies: 1
Views: 4,193
Posted By shunyip
edgeR works best with raw counts. You should use...

edgeR works best with raw counts. You should use tools like featureCounts or HTSeq with it.

Also, please note that there are a lot of newer software tools. Maybe you should take a look at tools...
Forum: RNA Sequencing 02-01-2017, 01:53 PM
Replies: 1
Views: 1,635
Posted By shunyip
Have you tried analyzing the PE dataset as a PE...

Have you tried analyzing the PE dataset as a PE dataset (don't trim them to the same length as SE and use both reads) to obtain expression data?
Forum: Bioinformatics 02-01-2017, 08:52 AM
Replies: 6
Views: 1,425
Posted By shunyip
Then, it would seem that an easy way for you is...

Then, it would seem that an easy way for you is to use bedtools.

You can convert a gtf file to bed file using:
cut -f 1,4,5,9 yourfile.gtf > yourfile.bed

This extracts the 1st, 4th, 5th and...
Forum: Bioinformatics 02-01-2017, 07:37 AM
Replies: 6
Views: 1,425
Posted By shunyip
Hi Capricy, You can supply your gene...

Hi Capricy,

You can supply your gene annotation (reference.gtf) to Cufflinks during assembly, using the -g argument.
Or you can use bedtools intersect to overlap and combine your merged.gtf and...
Forum: Bioinformatics 01-31-2017, 10:21 PM
Replies: 6
Views: 1,425
Posted By shunyip
RNA molecules can suffer from degradation....

RNA molecules can suffer from degradation. However, introns are identified by splice junctions and are often in the middle of the RNA reads. So, it is more likely for introns to be identified...
Forum: RNA Sequencing 01-31-2017, 08:34 AM
Replies: 2
Views: 1,462
Posted By shunyip
Hello Michel, While your way of doing it can...

Hello Michel,

While your way of doing it can be correct, maybe you can use a much simpler way to perform this analysis.

For example, you can extract DiseaseDisease1.TreatmentNone and...
Forum: Bioinformatics 01-31-2017, 07:57 AM
Replies: 2
Views: 1,302
Posted By shunyip
Another alternative is: x <-...

Another alternative is:
x <- read.csv("~/Configuration/Desktop/Chapter1/TFs.csv", row.names=1)
Forum: Academic/Non-Profit Jobs 05-08-2016, 11:31 PM
Replies: 0
Views: 734
Posted By shunyip
Postdoctoral/Informatics Specialist Position in Bioinformatics, Mayo Clinic

Link: https://www.iscb.org/cms_addon/jobs/job_details.php?id=5053

Dr. Junwen John Wang’s lab (http://jjwanglab.org) at Mayo Clinic Arizona is recruiting outstanding candidates for...
Forum: Bioinformatics 05-12-2015, 12:03 AM
Replies: 1
Views: 1,651
Posted By shunyip
No, it doesn't work. Please look at FPKM's...

No, it doesn't work. Please look at FPKM's formula.

Instead, you should sum up the raw counts of your gene and then use it to calculate its FPKM.
Forum: Bioinformatics 05-11-2015, 11:57 PM
Replies: 1
Views: 708
Posted By shunyip
You can first download a BED file from...

You can first download a BED file from https://genome.ucsc.edu/cgi-bin/hgTables?org=human

and then write a script to extract the genes that you are looking at.
Forum: RNA Sequencing 03-31-2015, 11:25 PM
Replies: 5
Views: 2,208
Posted By shunyip
In this paper, "Anders, S., McCarthy, D. J.,...

In this paper,
"Anders, S., McCarthy, D. J., Chen, Y., Okoniewski, M., Smyth, G. K., Huber, W., & Robinson, M. D. (2013). Count-based differential expression analysis of RNA sequencing data using R...
Forum: SOLiD 08-08-2014, 03:35 AM
Replies: 1
Views: 4,702
Posted By shunyip
Post Convert 0123 into nucleotides from a SOLiD srf file.

I downloaded some .srf files from GEO, which are RNA-seq data. By using the Staden Package, I was able to do the followings

When I use srf_dump_all, the results look like this:

[Info]
...
Forum: Bioinformatics 07-10-2014, 02:24 AM
Replies: 2
Views: 760
Posted By shunyip
Maybe you can filter your genomic scaffolds into...

Maybe you can filter your genomic scaffolds into coding-genes-only by using gene annotation files from UCSC.
Forum: De novo discovery 01-16-2014, 11:40 PM
Replies: 5
Views: 2,099
Posted By shunyip
A Quote from trimmomatic's website: "Illumina...

A Quote from trimmomatic's website:
"Illumina adapter and other technical sequences are copyrighted by Illumina,but we have been granted permission to distribute them with Trimmomatic. Suggested...
Forum: De novo discovery 01-16-2014, 07:26 PM
Replies: 5
Views: 2,099
Posted By shunyip
If FastQC couldn't find any adapters, they might...

If FastQC couldn't find any adapters, they might had been trimmed for you. However, if you have a HCC, it doesn't hurt to trim them on your own just in case, since trimming is a pretty fast step....
Forum: Bioinformatics 01-08-2014, 01:10 AM
Replies: 10
Views: 7,158
Posted By shunyip
Agreed, you may have run out of disk space. How...

Agreed, you may have run out of disk space. How much free memory do you have in your hard drive?
Forum: Bioinformatics 01-06-2014, 11:33 PM
Replies: 10
Views: 7,158
Posted By shunyip
Hello Arcolombo, I believe the problem is...

Hello Arcolombo,

I believe the problem is your genome file, just as you are suspecting. A genome file should be called "genome.fa".

I hope this post will help you find what you need:...
Forum: Bioinformatics 12-18-2013, 11:37 PM
Replies: 4
Views: 1,761
Posted By shunyip
At the FAQ section of Oases' manual, they...

At the FAQ section of Oases' manual, they suggested several more ways for you to decrease the memory usage also.
http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf

Hopefully it helps,
Forum: Bioinformatics 12-18-2013, 10:17 PM
Replies: 4
Views: 1,761
Posted By shunyip
Many HPCs have a setting that limits the maximum...

Many HPCs have a setting that limits the maximum amount of ram that you can use in a job. If your job exceed that amount, it will be killed. In this case, it is 268435456kb.

It appears that this...
Forum: Bioinformatics 11-20-2013, 11:41 PM
Replies: 1
Views: 863
Posted By shunyip
One common way to do it is to convert it back to...

One common way to do it is to convert it back to fastq format and trim it with Fastx-Toolkit or Trimmomatic.
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