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Search: Posts Made By: Fernas
Forum: Bioinformatics 10-01-2015, 08:20 AM
Replies: 5
Views: 882
Posted By Fernas
@blancha: I tried Biomart and could convert only...

@blancha: I tried Biomart and could convert only 8 IDs because the IDs are in miRBase format.
Forum: Bioinformatics 10-01-2015, 08:08 AM
Replies: 5
Views: 882
Posted By Fernas
Thank you very much indeed @blancha and...

Thank you very much indeed @blancha and @GenoMax!.

Regarding @blancha comments:
1) I already tried DAVID before but it could not recognize the mRNA ids that I have (e.g. hsa-miR-23a-3p,...
Forum: Bioinformatics 09-30-2015, 01:11 PM
Replies: 5
Views: 882
Posted By Fernas
Identify mRNA GEO terms and Functions

I have a list of 50 human mRNAs and I want to study their functional characteristics. Is there a database/website that can provide me with their GO terms? what about the GO terms of all human mRNAs...
Forum: Bioinformatics 02-09-2015, 10:20 PM
Replies: 1
Views: 956
Posted By Fernas
Problem in Using Tophat with Cutadapt output

I have fastq reads represented in SOLiD format (Reads are stored in two files, one in fasta format for reads, and another one contains qualities). here is an example for one read (I combined the read...
Forum: Bioinformatics 01-31-2015, 04:41 AM
Replies: 1
Views: 1,112
Posted By Fernas
Is there a difference between RNAseq and CAGE data analysis?

I have N fastq files for some samples. some were generated using RNA-Seq technology and some other were generated by sequencing CAGE libraries.

I am about to start processing all these files...
Forum: Bioinformatics 01-30-2015, 02:42 AM
Replies: 3
Views: 1,462
Posted By Fernas
Tophat Does not Work with SOLiD Reads

I have been trying for several weeks to run Tophat on SOLiD reads but I got the same error message every time. While I searched a lot of forums and related questions but could not find a solution.
...
Forum: Bioinformatics 01-20-2015, 05:57 AM
Replies: 1
Views: 713
Posted By Fernas
Identify TFs in New Assembled Organism

A denovo assembly of a new organism that lives in the sea (from the animal kingdom but we do not know its type specifically) have been prepared.

We want now to identify all possible transcription...
Forum: Bioinformatics 01-03-2015, 04:13 AM
Replies: 3
Views: 1,280
Posted By Fernas
Thank @GenoMax. Actually, I have 100 fastq...

Thank @GenoMax.
Actually, I have 100 fastq files. 95 of them contain quality values encoded in Phred33 (so I processed them with Trimmomatic), while 5 files are Color-space. I wanted to use...
Forum: Bioinformatics 01-03-2015, 02:19 AM
Replies: 3
Views: 1,280
Posted By Fernas
Can Trimmomatic handle Colorspace Reads

I have a RNASeq fastq file (first 4 lines are):
=====
@SRR179591.1.1 mendel_20110320_FRAG_BC_Ryan_RNA_Seq_2_58_235_F3 length=50
T.33.2010.0313.1231222320.1.3312.0.12.0212.0.013000
+SRR179591.1.1...
Forum: Bioinformatics 12-31-2014, 09:51 AM
Replies: 3
Views: 833
Posted By Fernas
Thank you very much indeed @mastal and @AJERYC...

Thank you very much indeed @mastal and @AJERYC and sorry for late reply.
I used Trimmomatic and it works fine!
Forum: Bioinformatics 12-13-2014, 12:23 AM
Replies: 19
Views: 5,087
Posted By Fernas
It works now. Thank you very much indeed Brian!.

It works now.
Thank you very much indeed Brian!.
Forum: Bioinformatics 12-12-2014, 06:40 AM
Replies: 19
Views: 5,087
Posted By Fernas
Thanks very much Brian. I downloaded BBMap...

Thanks very much Brian.

I downloaded BBMap and when I tried to run (bbcountunique.ssh) I got the following error "Exception in thread main java.lang.unsupportedclassversionerror:...
Forum: Bioinformatics 12-10-2014, 12:36 PM
Replies: 19
Views: 5,087
Posted By Fernas
How to plot the Saturation curves to assess the sequencing depth?

Dear all,

I want to know if there is a tool or ready-script that I can use to plot the Saturation (Rarefaction) plot in order to assess the sequencing depth of the sequenced libraries that I have.
Forum: Bioinformatics 12-08-2014, 12:32 AM
Replies: 3
Views: 833
Posted By Fernas
Do not know Adapters inside Sequences

I have ~100 Bissulfite-Seq fastq files and ~100 RNA-Seq fastq files representing many samples. All of the seq files were produced by Illumina tech.
I want to pre-process the fastq files by removing...
Forum: Bioinformatics 11-12-2014, 05:23 AM
Replies: 8
Views: 1,433
Posted By Fernas
Thanks very much @dpryan for your replies and the...

Thanks very much @dpryan for your replies and the suggestions
Forum: Bioinformatics 11-12-2014, 05:18 AM
Replies: 2
Views: 1,178
Posted By Fernas
Thank you very much @dpryan for the very...

Thank you very much @dpryan for the very informative reply. I will have a look into these tools.
Forum: Bioinformatics 11-12-2014, 05:13 AM
Replies: 8
Views: 1,433
Posted By Fernas
I agree with you if you mean that HTSeq-count is...

I agree with you if you mean that HTSeq-count is intended to generate expression matrix for detection of differentially expressed genes. Unfortunately, this is just one single applications, while,...
Forum: Bioinformatics 11-12-2014, 05:08 AM
Replies: 8
Views: 1,433
Posted By Fernas
Thanks @dpryan. I agree with you that we do not...

Thanks @dpryan. I agree with you that we do not need to shrink, however, I suggested this to avoid eliminating reads from being counted by HTSeq count. Actually, I do not like the ambiguity approach...
Forum: Bioinformatics 11-12-2014, 05:05 AM
Replies: 2
Views: 1,178
Posted By Fernas
Ambiguous Reads Treatment by HTSeq-Count

Currently, if a person uses HTSeq-Count to count reads on transcript level and the tool finds a read that overlaps two overlapped transcripts (this is very common) then the tool will identify the...
Forum: Bioinformatics 11-12-2014, 05:01 AM
Replies: 8
Views: 1,433
Posted By Fernas
Thank you very much @dpryan. I think I will write...

Thank you very much @dpryan. I think I will write this code. I guess it is simple but needs more careful analysis. This is because we need to check for each gene (or transcript) if the new upstream...
Forum: Bioinformatics 11-12-2014, 04:18 AM
Replies: 8
Views: 1,433
Posted By Fernas
Modify GENCODE GTF File for HTSeq

I want to run HTSeq on count number of mapped mRNA reads on Human genes (GENCode GTF file). However, I have to modify this gtf file because I want to allow a search region of an offset of -200 bp...
Forum: Bioinformatics 11-02-2014, 01:21 AM
Replies: 2
Views: 887
Posted By Fernas
Thank you very much @lindenb. That was of great...

Thank you very much @lindenb. That was of great help for me!.
Forum: Bioinformatics 10-30-2014, 04:33 AM
Replies: 2
Views: 887
Posted By Fernas
How to get GC positions in hg19

I want to get all the coordinates (positions) of the GC in the entire genome hg19 as a bed file (or similar format). Is there a tool to do that? or I have to write a script to read the fasta file and...
Forum: Bioinformatics 08-24-2014, 02:11 PM
Replies: 0
Views: 908
Posted By Fernas
2D and 3D numerical Properties of Domains

Hi All,

I have 2 transcription factors (each of them have 2 domains predicted by pfam). I want to know if anyone know of some databases/methods that contain numerical properties of domains...
Forum: Bioinformatics 08-16-2014, 12:29 PM
Replies: 365
Views: 156,130
Posted By Fernas
Hi All, How to cite FASTQC in my journal...

Hi All,

How to cite FASTQC in my journal paper? is it published somewhere? or we just refer to the URL of the tool?

Regards,
Showing results 1 to 25 of 74

 


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