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Forum: RNA Sequencing 06-21-2016, 01:53 AM
Replies: 2
Views: 1,314
Posted By daanum
RNASeq- Which method appropriate for Normalization?

Hi,
This question is to the people who have worked with RRBS methylation data and RNASeq data. I have RRBS methylation data for cell lines and the RNASeq data for the same cell lines. For RNASeq...
Forum: RNA Sequencing 05-27-2016, 04:49 PM
Replies: 4
Views: 3,641
Posted By daanum
Thanks. I did not understand this when you say...

Thanks. I did not understand this when you say trimmomatic keeps paired reads when option keepbothreads is set to 'true'.could you please graphically explain what it does? I am new to rnaseq so...
Forum: RNA Sequencing 05-26-2016, 06:55 PM
Replies: 4
Views: 3,641
Posted By daanum
Any suggestions on this will be greatly...

Any suggestions on this will be greatly appreciated.
Forum: RNA Sequencing 05-25-2016, 06:54 PM
Replies: 12
Views: 1,616
Posted By daanum
I will be using trimmomatic now,thanks for all...

I will be using trimmomatic now,thanks for all the help.
Forum: RNA Sequencing 05-25-2016, 06:46 PM
Replies: 4
Views: 3,641
Posted By daanum
Trimmomatic Unpaired files

Hi,

I run the following command in Trimmomatic:
java -jar /home/devgen/bin/trimmomatic-0.36.jar PE -phred33 C95VLANXX-2046D-01-01-01_L003_R1.fastq C95VLANXX-2046D-01-01-01_L003_R2.fastq ...
Forum: RNA Sequencing 05-23-2016, 03:08 AM
Replies: 12
Views: 1,616
Posted By daanum
I used a in-house script (cleanadaptors) to trim...

I used a in-house script (cleanadaptors) to trim the raw fastq files. I run the command to trim the data in the following way:

cleanadaptors -I /home/jmotwani/RNASeq/contam.fa -q 20 -x 25 -F...
Forum: RNA Sequencing 05-23-2016, 02:22 AM
Replies: 12
Views: 1,616
Posted By daanum
Thank you. The command worked this time but...

Thank you. The command worked this time but partly :(
Command :

tophat2 --num-threads 5 --mate-inner-dist 62 --library-type fr-firststrand --GTF ...
Forum: RNA Sequencing 05-22-2016, 10:55 PM
Replies: 12
Views: 1,616
Posted By daanum
I tried the following: tophat2 -p 5 -r 62 ...

I tried the following:

tophat2 -p 5 -r 62 -–library-type fr-firststrand --GTF /home/jmotwani/mydata/Genomes/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/gene.gtf –o...
Forum: RNA Sequencing 05-22-2016, 04:26 PM
Replies: 12
Views: 1,616
Posted By daanum
The Bowtie2Index folder has following files: ...

The Bowtie2Index folder has following files:

genome.1.bt2
genome.2.bt2
genome.3.bt2
genome.4.bt2
genome.fa
genome.rev.1.bt2
genome.rev.2.bt2
tophat_out
Forum: RNA Sequencing 05-22-2016, 03:56 PM
Replies: 12
Views: 1,616
Posted By daanum
Thanks Genomax. I removed the...

Thanks Genomax.

I removed the BOWTIE2_INDEXES option and gave the path as suggested above but I still get the same error.

I am wondering if its due to Bowtie2 index version incompatibility. Any...
Forum: RNA Sequencing 05-22-2016, 02:31 AM
Replies: 12
Views: 1,616
Posted By daanum
Unable to run Tophat2

Hi,

I am unable to run Tophat2 as I get an error.

Here is the command I run: tophat2 -p 5 -r 62 –library-type fr-firststrand -G...
Forum: Bioinformatics 04-27-2016, 09:14 PM
Replies: 1
Views: 878
Posted By daanum
Any suggestions on my questions?

Any suggestions on my questions?
Forum: Bioinformatics 04-21-2016, 09:42 PM
Replies: 1
Views: 878
Posted By daanum
Analysis of Methylation data

Hi,

I have preprocessed, aligned and filtered by RRBS methylation data.

I would like to know what are the best possible tools available to present my methylation data to show the pattern of my...
Forum: Bioinformatics 04-12-2016, 09:45 PM
Replies: 5
Views: 1,117
Posted By daanum
Thanks Genomax. Hi SJ, Sorry for the...

Thanks Genomax.

Hi SJ,

Sorry for the confusion, please post your reply in this thread (if you still can't PM me)
Thanks.
Forum: Bioinformatics 04-12-2016, 02:10 PM
Replies: 5
Views: 1,117
Posted By daanum
Thanks Genomax. I will follow up in the new...

Thanks Genomax. I will follow up in the new thread.

Thanks SJ. PM settings are already enabled in my account. Could you please email me the suggestions in a new thread that Genomax has created ?
...
Forum: Bioinformatics 04-11-2016, 07:49 PM
Replies: 5
Views: 1,117
Posted By daanum
Tools available for analyzing the methylation dataset for Human DNA Methylation 3x720

Hi,

I am unable to find a link to start a new thread so I am posting my question here, sorry.

I am working with Nimblegen DNA methylation datasets. Can any one please help with any tools...
Forum: RNA Sequencing 03-13-2016, 08:03 PM
Replies: 6
Views: 1,790
Posted By daanum
Questions about RNASeq

Hi,

I have a question regarding the RNASeq.
I am working with Human cell lines. For RNA Seq :
i) Should I consider Paired end sequencing or Single end?

ii) I am planning to get the sequencing...
Forum: Bioinformatics 02-25-2016, 06:15 PM
Replies: 3
Views: 4,492
Posted By daanum
Hi, How do I interpret the image of a...

Hi,

How do I interpret the image of a hierarchical tree attached here?
The tree is created with euclidean distance using complete linkage method.

Thanks.
Forum: Bioinformatics 02-20-2016, 08:42 PM
Replies: 2
Views: 1,695
Posted By daanum
Thumbs up Clustering samples of RRBS data

Hi,

I would like to see if the biological replicates of my two groups fall together. Is there a simple tool to check the clustering of samples. i am working with methylation data using RRBS...
Forum: Bioinformatics 02-10-2016, 05:46 PM
Replies: 23
Views: 42,397
Posted By daanum
How can i sort multiple BAM files using samtools?

Hi,

Is there any way to sort multiple bam files at the same time using samtools?
Thanks.
Forum: Bioinformatics 02-09-2016, 12:10 AM
Replies: 366
Views: 193,651
Posted By daanum
Hi , I am using a Linux GNU server. How can...

Hi ,

I am using a Linux GNU server. How can I view the.html files which are generated as a result of fastqc, on the linux server?
Thank you.
Forum: Bioinformatics 11-08-2015, 11:04 PM
Replies: 649
Views: 180,764
Posted By daanum
Hi, I am unable to run the...

Hi,

I am unable to run the bismark_genome_preparation step yet.
I get an error "Command not found'.
Any idea? I am trying since yesterday, not sure what am i doing wrong?

:mad::mad:
Forum: Sample Prep / Library Generation 11-07-2015, 11:39 PM
Replies: 1
Views: 793
Posted By daanum
How to detect if the sample is bisulphie converted?

Hi,

I am working with RRBS methylation data. At the moment I have got the sequencing done and have the FAST QC results of all the sequenced samples.

There was one sample during bisulphite...
Forum: Bioinformatics 11-07-2015, 12:12 PM
Replies: 649
Views: 180,764
Posted By daanum
Unhappy genome preparation

hi,
I am trying to run bismark genome preparation but unable to do so.
I have bismark v 14.5 unzipped folder on server and have bowtie-2.2.2.6 version unzipped folder and genome files for human...
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