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Search: Posts Made By: tinguzman
Forum: Bioinformatics 09-14-2015, 07:47 PM
Replies: 1
Views: 1,194
Posted By tinguzman
change default FDR on edgeR

Hi,

Could anyone please tell me how to change the FDR from default (0.05) to 0.0001 in edgeR?

et <- exactTest(y, pair=c("1","2"))
out.adjusted <- topTags(et, n=Inf, adjust.method="BH")...
Forum: Bioinformatics 09-12-2015, 02:40 AM
Replies: 1
Views: 1,412
Posted By tinguzman
topGO factor with 2 levels

Hi,

I'm trying to do GO enrichment analysis using topgo, but i've encountered a problem, read below. what does factor w/ level 1 mean? it says that i should have 2 level factors.

geneNames...
Forum: Bioinformatics 09-10-2014, 09:10 PM
Replies: 1
Views: 1,573
Posted By tinguzman
TopGo, factor of 1 means

Hi,

I'm trying to do GO enrichment analysis using topgo, but i've encountered a problem, read below. what does factor w/ level 1 mean? it says that i should have 2 level factors. how can I fix...
Forum: Bioinformatics 09-10-2014, 07:32 PM
Replies: 2
Views: 2,552
Posted By tinguzman
Hi again, I loaded the custom annotation...

Hi again,

I loaded the custom annotation successfully, however when I tried to load my list of DEGs with Pvalues, I again encountered an error


DEGs PValue
c33534_g1 2.61E-239...
Forum: Bioinformatics 09-10-2014, 07:15 PM
Replies: 2
Views: 2,552
Posted By tinguzman
loading custom annotation on topgo

Hi,

I'm stuck on loading my customize annotation on topgo using R. I have a .txt file containing list of genes and their GO Ids.

Genes Gene ontology IDs
c10020_g1 GO:0047021; GO:0019369;...
Forum: Bioinformatics 09-04-2014, 12:05 AM
Replies: 0
Views: 625
Posted By tinguzman
extract GO enrichment

Hi,

i'm trying to use the extract_GO_enrichment script on the trinity package. however, i'm not sure on what information to use as inputs.

--GO_annots - this is the file containing list of...
Forum: RNA Sequencing 08-14-2014, 04:19 AM
Replies: 1
Views: 1,294
Posted By tinguzman
removing genes with low level expression

Hi,

I'm currently using the trinity package for RNAseq analysis. A little help here. If I wanted to run EdgeR with all the genes in my trinity assembly, is there a way to filter the DE results to...
Forum: Bioinformatics 08-12-2014, 08:22 PM
Replies: 0
Views: 960
Posted By tinguzman
isopct_cutoff on filter_by_rsem_values.pl

Hi,

how does the isopct_cutoff works? I know that it will filter transcripts, keeping those with isoform percentage values equal to or greater than this. What would be the best value to start of....
Forum: Bioinformatics 08-06-2014, 02:54 AM
Replies: 17
Views: 1,824
Posted By tinguzman
Hi Ryan, thank you very much. submitted...

Hi Ryan,

thank you very much. submitted fastq files or sra files are not yet trimmed/filtered right? they are raw sequences, for example from illumina sequencing.

best,
christine
Forum: Bioinformatics 08-06-2014, 02:39 AM
Replies: 17
Views: 1,824
Posted By tinguzman
hi again! i just finished running...

hi again!

i just finished running ./fastq-dump.2.3.5.2 -split-files ./SRR504687.sra. i have 2 output SRR504687_1 and SRR504687_2. one is 13gb while the other is only 3gb. i'm expecting that they...
Forum: Bioinformatics 08-06-2014, 01:25 AM
Replies: 17
Views: 1,824
Posted By tinguzman
Hi, thanks a lot! it's working now. ...

Hi,

thanks a lot! it's working now.

best,
christine
Forum: Bioinformatics 08-06-2014, 01:04 AM
Replies: 17
Views: 1,824
Posted By tinguzman
Hi thanks for your reply. I ran this...

Hi

thanks for your reply. I ran this command, within the bin directory, - perl fastq-dump.2.3.5.2 SRR504687.sra. I also copied the sra file to the bin.

I downloaded this rsa file from here...
Forum: Bioinformatics 08-05-2014, 11:54 PM
Replies: 17
Views: 1,824
Posted By tinguzman
SRA to fastq

Hi,

I'm trying to convert an sra file to fastq. i downloaded the sra toolkit and ran fastq-dump, here's what i got:


"Unrecognized character \xCF; marked by <-- HERE after <-- HERE near column...
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