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Search: Posts Made By: Trudy
Forum: Bioinformatics 02-07-2013, 07:51 AM
Replies: 13
Views: 3,171
Posted By Trudy
But the number 36,497,412 is relative to R1 and...

But the number 36,497,412 is relative to R1 and R2 fastq file together?
Forum: Bioinformatics 02-07-2013, 07:48 AM
Replies: 1
Views: 1,040
Posted By Trudy
Exclamation Problem with Cuffcompare to integrate different annotation sources

Hi bioinformatics community!

I have a problem with cuffcompare.
I have different gtf files and I want to integrate them to create a new annotation.
This goal is not impossible and I obtained...
Forum: Bioinformatics 12-03-2012, 07:22 AM
Replies: 0
Views: 892
Posted By Trudy
RABT assembly output

Hello!

I've a question about the output of cufflinks with RABT assembly.
In the isoforms.fpkm_tracking file I have 3 different situations:

1) ENST00000492842 - - ENSG00000240361 if...
Forum: RNA Sequencing 12-19-2011, 06:19 AM
Replies: 0
Views: 1,082
Posted By Trudy
difference fpkm_tracking file

Hi all,
I have a question about difference between fpkm_tracking file from cufflinks quantification and cuffdiff differential expression.
I don't understand why the same gene in genes.fpkm_tracking...
Forum: RNA Sequencing 10-19-2011, 08:40 AM
Replies: 0
Views: 1,442
Posted By Trudy
Exclamation Cufflinks quantification and Cuffdiff output

Hello!!!

I used Cufflinks for quantification and for differential expression analysis but I have an important question:
I obtained FPKM quantification values for each sample like this:...
Forum: Bioinformatics 06-22-2011, 06:56 AM
Replies: 1
Views: 1,258
Posted By Trudy
Exclamation coverage RNAseq

I would like to determine the coverage of mapped reads in exons, introns and intergenic regions.
Are there tools that could help me?

Thanks
Forum: Bioinformatics 06-13-2011, 02:20 AM
Replies: 0
Views: 1,174
Posted By Trudy
cufflinks quantification problem

Hi all,

I have a question about quantification with Cufflinks.
I've performed a quantification analysis with Cufflinks in two ways.
I've 4 samples for Population (samples are biological...
Forum: Bioinformatics 05-24-2011, 02:01 PM
Replies: 1
Views: 2,675
Posted By Trudy
Question Help me!!!!! low % of properly paired reads!!!

Hi all,
I have an important question:
I have 75x2 reads from Illumina HiScan and I preformed:

-alignment with TopHat
-samtools flagstat to know the % of properly paired reads

This % very...
Forum: Bioinformatics 05-19-2011, 03:10 AM
Replies: 1
Views: 1,628
Posted By Trudy
Exclamation Tophat singleton behaviour & Flagstats output

Dear all,

I have a paired end (2x75) Illumina data and I aligned these reads with TopHat v1.2.0.
I performed a samtools flgstat analysis of my files.bam and an output example is:

5033547 in...
Forum: Bioinformatics 04-05-2011, 06:06 AM
Replies: 0
Views: 759
Posted By Trudy
bundle_id Cufflinks

Hi!!!

What is the bundle_id value in transcript.expr file produce by Cufflinks?

thanks
Forum: Bioinformatics 04-04-2011, 05:32 AM
Replies: 7
Views: 4,691
Posted By Trudy
How do you solve this problem? I have the same...

How do you solve this problem?
I have the same problem..Could you help me?

ARTEMIS doesn't load my bam file..
I sorted and indexed the file.bam with samtools.....but the problem persist!

help...
Forum: Bioinformatics 04-01-2011, 04:44 AM
Replies: 1
Views: 1,780
Posted By Trudy
TopHat file.bam file.bed join

Hi all,

I have a question about TopHat alignment.

I have 4 sample alignments and I want to join all together in a only 1 file alignment because these sample belong to the same population (same...
Forum: Bioinformatics 03-29-2011, 12:23 AM
Replies: 4
Views: 32,686
Posted By Trudy
Look this: ...

Look this:

http://cufflinks.cbcb.umd.edu/howitworks.html

"In RNA-Seq experiments, cDNA fragments are sequenced and mapped back to genes and ideally, individual transcripts. Properly normalized,...
Forum: Bioinformatics 03-23-2011, 05:43 AM
Replies: 2
Views: 1,178
Posted By Trudy
calibrated quality string "B" full

Hello everybody!

I have a question about the calibrated quality string in qseq.txt file.

If I have full called sequence BUT a calibrated quality string full of B and the read passes the...
Forum: Bioinformatics 03-23-2011, 02:44 AM
Replies: 4
Views: 2,709
Posted By Trudy
Alignment PE reads with different length by TopHat

Hello!
I want to know if TopHat 1.2.0 can work with paired-end reads of different lenght without problems.
Can I modify the -r/--mate-inner-dist for correct output?

Example: I have sample with...
Forum: Introductions 03-23-2011, 02:38 AM
Replies: 1
Views: 1,417
Posted By Trudy
Alignment PE reads with different length by TopHat

Hello!
I want to know if TopHat 1.2.0 can work with paired-end reads of different lenght without problems.
Can I modify the -r/--mate-inner-dist for correct output?

Example: I have sample with...
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