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Forum: Bioinformatics 03-28-2016, 06:46 PM
Replies: 0
Views: 513
Posted By mathew
Smile Question about Seqmonk

I am running my analysis through Seqmonk. I want to use a filter where I want to select features/ genes with at least 2 reads in all samples. After running the RNA seq workflow the counts will...
Forum: Bioinformatics 06-23-2015, 04:51 AM
Replies: 312
Views: 89,130
Posted By mathew
.dat file will give the genome coordinates of...

.dat file will give the genome coordinates of that particular gene. If I create a report that will be for one annotation i.e either TSS 2000(say) bp up down / mRNA/ CGI / intergenic and so on. What I...
Forum: Bioinformatics 06-22-2015, 05:13 PM
Replies: 312
Views: 89,130
Posted By mathew
Question about Seqmonk annotations

I am using Seqmonk 30. I have ran Chip analysis and has annotations like CGI, TSS, mRNA, Promoter etec. I want to export coordinates with all the annotations in one file Is it possible how to get...
Forum: Bioinformatics 02-09-2014, 03:59 PM
Replies: 312
Views: 89,130
Posted By mathew
FastQc for Bisulfite seq

Two related questions:
1.Can we used FAstqc for qc check of bisulfite seq data. Will it give me CG ratios etc?
2. I have used Seq monk but have not used Bismark. Is there a GUI version Bismark...
Forum: Bioinformatics 01-24-2014, 03:19 PM
Replies: 312
Views: 89,130
Posted By mathew
CAn I save wiggle file

Hi Simon,

I ran ChIP seq analysis and created a wiggle file to look for peaks. Can I export the wiggle track file or not at all.
Thanks
Forum: Bioinformatics 10-03-2013, 09:27 AM
Replies: 312
Views: 89,130
Posted By mathew
Correlation coefficient in cluster

I have question about seqmonk- when we perform clustering on any analyzed data then we can have different subsets of clusters based upon correlation coefficient. How it calculate correlation...
Forum: Bioinformatics 09-08-2013, 09:18 PM
Replies: 312
Views: 89,130
Posted By mathew
I am curious if Seqmonk can give me coverage of...

I am curious if Seqmonk can give me coverage of specific genes/ transcripts from DNA seq data as is given by coverageBed in bedtools http://bedtools.readthedocs.org/en/latest/
I want to calculate...
Forum: Bioinformatics 09-08-2013, 03:10 PM
Replies: 1
Views: 1,389
Posted By mathew
TCGA data access

I have read various posts including thsi one about TCGA-
http://seqanswers.com/forums/showthread.php?t=19657
I never had my luck in accessing the TCGA data. However I recently read one post-...
Forum: Bioinformatics 08-12-2013, 08:11 AM
Replies: 312
Views: 89,130
Posted By mathew
Seqmonk and Java

Simon,

The Java and seqmonk problem is now creating a real headache. I am also in same boat. Perhaps at some point in time Seqmonk and Java dependency need to be thoroughly investigated. I...
Forum: Bioinformatics 06-10-2013, 08:52 PM
Replies: 312
Views: 89,130
Posted By mathew
I am using Seqmonk for analysis of RNAseq PE...

I am using Seqmonk for analysis of RNAseq PE reads. When I run pipeline will use option of getting raw rpkm, will it give me fpkm values if I use PE reads. Thanks.
Forum: Bioinformatics 05-26-2013, 05:21 PM
Replies: 312
Views: 89,130
Posted By mathew
Mitochondrial genome in seqmonk

I have a chipseq data where mouse mitochondria fractions are enriched However, I think mitochondrial Chr is not there in the genome when we download the genome with in Seqmonk. How can I have M...
Forum: Bioinformatics 04-12-2013, 12:44 AM
Replies: 312
Views: 89,130
Posted By mathew
intergenic regions in bacteria

I have a RNA seq data from a bacteria. I was wondering if I can design (quantitate) probes for intergenic regions? Or is there an alternative way of extracting that information from seqmonk?

Thanks
Forum: Bioinformatics 03-19-2013, 10:54 AM
Replies: 312
Views: 89,130
Posted By mathew
long noncoding RNA detection and quantification

Thanks Simon,

Will it include specifically long noncoding RNA?
Forum: Bioinformatics 03-16-2013, 11:54 AM
Replies: 312
Views: 89,130
Posted By mathew
seqmonk intergenic probes

Can Seqmonk map probes in intergenic region. To be more precise Can it help me in giving read counts in noncoding RNA directly/ indirectly:confused:?
Thanks.
Forum: Bioinformatics 03-10-2013, 12:57 PM
Replies: 312
Views: 89,130
Posted By mathew
question of Seqmonk

I am using seq monk for RNA-seq analysis and am looking for following question:

1. in Version 24 when I go to feature probe generator-feature to design around attenuator, what is this related to?...
Forum: Bioinformatics 03-05-2013, 06:05 AM
Replies: 1
Views: 721
Posted By mathew
chipseq for mitochondrial genes

I have a dataset where chipseq was performed and I am looking specifically for mitochondrial genes. Is there a special work flow which I may use or normal BWa aligners should be used and follow the...
Forum: Bioinformatics 03-03-2013, 06:35 AM
Replies: 312
Views: 89,130
Posted By mathew
time course RNA-seq with replicate

I was wondering is it possible to analyze (exon level) RNA-seq data with three replicates over a time course in Seqmonk.

Thanks
Forum: Sample Prep / Library Generation 02-27-2013, 05:32 AM
Replies: 5
Views: 2,369
Posted By mathew
long noncoding RNA detection and quantification experiment

Thanks Dario1994,
Consider me as new in this area and I am getting little confused with the literature available e.g http://mbio.asm.org/content/1/5/e00206-10.full
suggest that non-ribosomal RNA...
Forum: Sample Prep / Library Generation 02-26-2013, 06:35 AM
Replies: 5
Views: 2,369
Posted By mathew
noncoding RNA

What is the best practise for detection of novel long noncoding RNA as well as the expression of known lincRNA. A litertaure survey showed Ribo depleted, Ribo zero, Hexamer approaches. I wonder if...
Forum: Bioinformatics 01-04-2013, 12:37 PM
Replies: 3
Views: 2,187
Posted By mathew
miseq alignments

The genome is ~5K and we used Nextera DNA libraries and then seq with 2X250 bp. It appears that first I need to find out overlap two mates and then align?
BWA I used default option with my custom...
Forum: Bioinformatics 01-04-2013, 07:32 AM
Replies: 3
Views: 2,187
Posted By mathew
alignment of Miseq data

To identify presence and absence of a bacterial in clinical samples as well as sequence variation among various states of diseases if any; we recently generated 2X250bp miseq data. I used BWA it is...
Forum: Bioinformatics 12-18-2012, 09:23 AM
Replies: 312
Views: 89,130
Posted By mathew
scatter plot colors

Thanks Simon for quick reply So from the attached image - red area represents a perfect correlation (or close to 1) and as we move away from line it decrease.
Is it reasonable or I misunderstood...
Forum: Bioinformatics 12-18-2012, 08:26 AM
Replies: 312
Views: 89,130
Posted By mathew
I ahve a question about using scatter plot in...

I ahve a question about using scatter plot in seqmonk. When you scatter plot two read counts/ expression there is cloud of red dots in in the center what that mean? Alternatively Can someone point me...
Forum: Bioinformatics 12-17-2012, 06:25 AM
Replies: 34
Views: 16,314
Posted By mathew
Galaxy

I will vote for Galaxy as it is very user friendly and provide you the control on your analysis to certain extent not just a black box. If one invest some time one can get into through adjustment of...
Forum: Bioinformatics 12-08-2012, 07:24 PM
Replies: 6
Views: 3,853
Posted By mathew
Sliding window

krobison

Thanks for your help!!
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