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Forum: RNA Sequencing 04-16-2015, 06:02 AM
Replies: 2
Views: 2,045
Posted By aggp11
Depending on the overall library depth...

Depending on the overall library depth differences, using IGV to count and compare read counts might not give you accurate results.

Like mbblack mentioned, you'll need some replication to make any...
Forum: Bioinformatics 04-16-2015, 05:43 AM
Replies: 5
Views: 1,350
Posted By aggp11
Like Diego and Brian mentioned, you should try...

Like Diego and Brian mentioned, you should try longer reference sequences like the whole genome (if available for your species of interest) or the miRNA hairpin sequences (can be downloaded from...
Forum: Bioinformatics 02-27-2015, 06:00 AM
Replies: 15
Views: 11,594
Posted By aggp11
In my understanding, using spike-ins helps us...

In my understanding, using spike-ins helps us detect the "breadth" of our sequencing, or in other terms the low-abundant transcripts that can potentially be detected in the sequencing experiments (I...
Forum: RNA Sequencing 02-17-2015, 01:44 PM
Replies: 2
Views: 1,588
Posted By aggp11
As a quick analysis you could look at scatter...

As a quick analysis you could look at scatter plots of the read counts (hopefully normalized) and also perform some clustering analysis on the same to see reproducibility of your libraries.
Forum: Bioinformatics 02-17-2015, 01:39 PM
Replies: 9
Views: 1,905
Posted By aggp11
Like dpryan said, it might just be the case of...

Like dpryan said, it might just be the case of having the two conditions switched around that leads to the inverse fold change. You could check this using something like head(res_DESeq2) for the...
Forum: Bioinformatics 12-31-2014, 11:43 AM
Replies: 2
Views: 1,902
Posted By aggp11
Dear Wolfgang, Thank you for the response. ...

Dear Wolfgang,

Thank you for the response.

Praful
Forum: Bioinformatics 12-19-2014, 08:35 AM
Replies: 8
Views: 12,606
Posted By aggp11
DESeq2 log2 fold change discrepancy

Hi,

I am working with an RNA-Seq dataset and used DESeq2 to perform differential gene expression analysis using a multi-factor design.

In my results I noticed that the log2FC values were...
Forum: Bioinformatics 12-18-2014, 01:01 PM
Replies: 2
Views: 1,902
Posted By aggp11
DESeq2 for targeted RNA-Seq

Hi,

We plan to run some targeted whole transcriptome rna-seq using the AmpliSeq RNA methodology currently being sold by Life Technologies/Thermo Fisher. As a background on the technique, LT has...
Forum: Bioinformatics 12-15-2014, 07:34 AM
Replies: 11
Views: 1,904
Posted By aggp11
Thank you for the prompt reply.

Thank you for the prompt reply.
Forum: Bioinformatics 12-13-2014, 01:46 PM
Replies: 11
Views: 1,904
Posted By aggp11
If in the original question, we have more than 2...

If in the original question, we have more than 2 cell lines, and we want to compare the "global" differences between conditions c1 and c2 (still taking into account the fact that we have multiple...
Forum: RNA Sequencing 11-26-2014, 07:12 AM
Replies: 1
Views: 2,120
Posted By aggp11
Extract exon-intron reads from RNA-Seq data

Hi,

We are trying to look at potential DNA contamination in our RNA/cDNA libraries using the RNA-Seq data (single-end Ion Torrent). One method of doing this seems to be looking at reads that start...
Forum: Bioinformatics 11-03-2014, 06:47 AM
Replies: 3
Views: 1,605
Posted By aggp11
Hi, Would this mean that we create a BED...

Hi,

Would this mean that we create a BED file which has the start and end coordinates as the "END" of the previous exon and the "Start" of the next? Also, could you explain the incomplete overlap...
Forum: Academic/Non-Profit Jobs 07-03-2014, 08:58 AM
Replies: 20
Views: 3,663
Posted By aggp11
I am guessing that if somebody is thinking of...

I am guessing that if somebody is thinking of applying for a postdoc in Bioinformatics, they would have some knowledge about what Bioinformatics is. Is it too much to ask/assume that these smart...
Forum: RNA Sequencing 10-11-2013, 01:02 PM
Replies: 1
Views: 2,875
Posted By aggp11
Compare RNA-seq and qPCR results using bar plots with error bars

Hi,

We performed RNA-Seq on 3 biological replicates each for Control vs. Treated libraries. We used DESeq and got a list of significant DE genes. We have performed RT-qPCR for a subset of these...
Forum: Bioinformatics 08-09-2013, 08:28 AM
Replies: 7
Views: 3,440
Posted By aggp11
Sorry, if this seems too simple to be an issue,...

Sorry, if this seems too simple to be an issue, but did you check that the location of your features match in both the sam and GTF files?
Forum: Bioinformatics 07-05-2013, 07:22 AM
Replies: 2
Views: 3,746
Posted By aggp11
HTseq count for miRNA

Hi,

We did some miRNA sequencing (3 WT vs. 3 condition) and I would like to carry out differential expression analysis using DESeq (DESeq2). The alignment was done using the RNA-Star aligner (part...
Forum: Bioinformatics 05-06-2013, 10:14 AM
Replies: 6
Views: 1,593
Posted By aggp11
GenoMax, I think if the chromosome names...

GenoMax,

I think if the chromosome names don't match, bedtools neither returns an output nor reports an error. I am not sure about bamUtil as I have never used it before.
Forum: Bioinformatics 05-06-2013, 10:12 AM
Replies: 8
Views: 2,904
Posted By aggp11
Your intersectBed output suggests that you are...

Your intersectBed output suggests that you are using the Bam file converted to bed as "-a" and regions.bed as "-b". However, if you switch -a and -b files around, and then use -v, you'll get regions...
Forum: Bioinformatics 05-06-2013, 09:38 AM
Replies: 6
Views: 1,593
Posted By aggp11
Hi, Could you list the exact "error message"...

Hi,

Could you list the exact "error message" that both BedTools and BedUtils are reporting? May be a line or two in your file has more columns than the others. It'll be easier to troubleshoot with...
Forum: Bioinformatics 05-06-2013, 07:00 AM
Replies: 1
Views: 2,052
Posted By aggp11
Hi, Could you paste the first 5-10 lines of...

Hi,

Could you paste the first 5-10 lines of your GTF file here?
Forum: Epigenetics 05-02-2013, 02:02 PM
Replies: 6
Views: 4,535
Posted By aggp11
You could use bedtools' FastaFromBed utility by...

You could use bedtools' FastaFromBed utility by providing it your BED file and the whole genome reference FASTA file.
Forum: Bioinformatics 04-29-2013, 11:08 AM
Replies: 11
Views: 3,120
Posted By aggp11
Also, besides just aligning to the HLA region,...

Also, besides just aligning to the HLA region, you could also try aligning to the entire human genome (hg19). Hopefully this wouldn't lead to too many off-target alignment and you would be able to...
Forum: Bioinformatics 04-18-2013, 11:49 AM
Replies: 6
Views: 3,416
Posted By aggp11
Ok. So I ran your command on our system and I got...

Ok. So I ran your command on our system and I got the help menu with the following message:

Must supply REFERENCE_SEQUENCE when supplying PER_TARGET_COVERAGE

and so you need to provide your...
Forum: Bioinformatics 04-18-2013, 11:40 AM
Replies: 6
Views: 3,416
Posted By aggp11
I know this might be silly, but just try changing...

I know this might be silly, but just try changing the name of your PER_TARGET_COVERAGE file to not have "PER_TARGET_COVERAGE". may be just make it all lowercase.

I would be surprised if this...
Forum: Bioinformatics 04-15-2013, 09:56 AM
Replies: 11
Views: 3,350
Posted By aggp11
Could you print like 5-10 lines from your...

Could you print like 5-10 lines from your "combined" vcf file here? Try to include an example of what output you would like to see.
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