SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 36
Search took 0.00 seconds.
Search: Posts Made By: ea11
Forum: Bioinformatics 05-23-2016, 02:54 AM
Replies: 0
Views: 599
Posted By ea11
Cuffdiff problem

Hi,

I am attempting to run cuffdiff one some of my samples, using a custom gtf file that I created following the gtf file format, but I am having a problem running it. I am using cufflinks v2.2.1...
Forum: Bioinformatics 05-06-2016, 05:55 AM
Replies: 2
Views: 1,154
Posted By ea11
Thanks GenoMax, I'll have a look at the paper...

Thanks GenoMax, I'll have a look at the paper while I wait to see if anyone else know more about them.
Forum: Bioinformatics 05-06-2016, 04:18 AM
Replies: 2
Views: 1,154
Posted By ea11
Ensembl miRNA host genes

tmiI have been using a GTF file from Ensembl to get count table from HTSeq for an RNAseq experiment. Tables were inputted into DESeq2 and the resulting DE genes include microRNA host genes (e.g....
Forum: Bioinformatics 01-08-2016, 12:00 AM
Replies: 0
Views: 1,160
Posted By ea11
Picard tools error

Hi,

I am attempting to use CollectRnaSeqMetrics from picard tools on my BAM files but I am not being successful with it for some reason. Below is the code that I am using:

java -jar...
Forum: Bioinformatics 01-04-2016, 02:21 AM
Replies: 0
Views: 1,814
Posted By ea11
Design matrix for edgeR help

Hi,

I am attempting to create a design matrix in edgeR to determine differentially expressed genes, but I am unsure on the notation to use as I am relatively new to R and not a statistician in any...
Forum: Bioinformatics 11-10-2015, 10:02 AM
Replies: 29
Views: 2,455
Posted By ea11
Hi Brian, I tried lowering the memory, and it has...

Hi Brian, I tried lowering the memory, and it has worked. Thanks for your help. BBDuk has performed much better than cutadapt previously has for me.
Forum: Bioinformatics 11-10-2015, 05:37 AM
Replies: 29
Views: 2,455
Posted By ea11
We have been told to use the login nodes for any...

We have been told to use the login nodes for any jobs less than half an hour, which all the BBDuk jobs are.

And yea, I am already using the job scheduler for alignments and other jobs which...
Forum: Bioinformatics 11-10-2015, 05:07 AM
Replies: 29
Views: 2,455
Posted By ea11
Yea the job that fails does produce a file in the...

Yea the job that fails does produce a file in the specific output directory, but it is not the expected size (probably around half what it should be)

I have just tried running one of the files...
Forum: Bioinformatics 11-10-2015, 04:56 AM
Replies: 29
Views: 2,455
Posted By ea11
I am just trying the same job on a different...

I am just trying the same job on a different login node to see if it works on that
Forum: Bioinformatics 11-10-2015, 04:47 AM
Replies: 29
Views: 2,455
Posted By ea11
As this is a short job, I am not sending the job...

As this is a short job, I am not sending the job off and install I am running it on one of the login nodes.

I have tried doing the same job more than once and it keeps failing for some reason,...
Forum: Bioinformatics 11-10-2015, 04:40 AM
Replies: 29
Views: 2,455
Posted By ea11
Nope, that's one of the first things I checked. I...

Nope, that's one of the first things I checked. I still have 100GB storage available
Forum: Bioinformatics 11-10-2015, 04:32 AM
Replies: 29
Views: 2,455
Posted By ea11
Hi Brian, So I have decided to use BBDuk...

Hi Brian,

So I have decided to use BBDuk instead of BBDul2 and do it twice. The following is my code:

bash bbduk.sh in1=/PATH/M_R1_001.fastq.gz in2=/PATH/M_R2_001.fastq.gz...
Forum: Bioinformatics 11-09-2015, 11:06 AM
Replies: 29
Views: 2,455
Posted By ea11
Yea that is what I was expecting from the people...

Yea that is what I was expecting from the people who did the sequencing, which is why I was shocked when I was given 640 files rather than the 80 I was expecting.
Forum: Bioinformatics 11-09-2015, 10:58 AM
Replies: 29
Views: 2,455
Posted By ea11
Yea Geno, that was an option that we talked...

Yea Geno, that was an option that we talked through, but then as a lab group, we decided to merge all the files from the start and work on 2 per sample rather than 16 per sample
Forum: Bioinformatics 11-09-2015, 10:48 AM
Replies: 29
Views: 2,455
Posted By ea11
Yep, am currently finding out that zcatting takes...

Yep, am currently finding out that zcatting takes longer, which is why I'm running it overnight. I shall put forward a request to upgrade the version of Java that we have.

Thanks for you help Brian
Forum: Bioinformatics 11-09-2015, 10:40 AM
Replies: 29
Views: 2,455
Posted By ea11
Ok, I shall give BBDuk a look and see the results...

Ok, I shall give BBDuk a look and see the results of that.

With regards to the Java version, I'm running all my analysis on a computer cluster so the only version of Java installed by the...
Forum: Bioinformatics 11-09-2015, 10:23 AM
Replies: 29
Views: 2,455
Posted By ea11
Thanks for the reply Brian. I am zcatting the...

Thanks for the reply Brian. I am zcatting the files at the moment, so hopefully they should work like that, but would be nice to work out why my files didn't working just concatenating them.

java...
Forum: Bioinformatics 11-09-2015, 07:25 AM
Replies: 29
Views: 2,455
Posted By ea11
Ah right ok, thanks for the clarification. Well I...

Ah right ok, thanks for the clarification. Well I am re-merging the files using the command in the other post, and will hopefully wait to hear back from Brian when he gets round to it.

Thanks
Forum: Bioinformatics 11-09-2015, 06:52 AM
Replies: 29
Views: 2,455
Posted By ea11
Thanks for that, I shall give it a try and see if...

Thanks for that, I shall give it a try and see if it works.

The thing is though, when I run the concatenated file through fastqc, it shows the correct number of reads you would expect...
Forum: Bioinformatics 11-09-2015, 06:29 AM
Replies: 29
Views: 2,455
Posted By ea11
BBDuk2 not trimming whole file

Hi,

I am running BBDuk to trim adapters from my fastq files and remove reads with low quality. My RNAseq was PE and done on 8 lanes for each sample, so for each sample I have 8 forward read files...
Forum: Bioinformatics 11-06-2015, 03:52 AM
Replies: 6
Views: 2,411
Posted By ea11
Thanks, I shall have a read and see what the...

Thanks, I shall have a read and see what the results look like with BBDuk/BBMap while my tophat jobs are running
Forum: Bioinformatics 11-06-2015, 03:46 AM
Replies: 6
Views: 2,411
Posted By ea11
Nope I am not. R1 files are before the R2 files...

Nope I am not. R1 files are before the R2 files in the script.
Forum: Bioinformatics 11-06-2015, 03:37 AM
Replies: 6
Views: 2,411
Posted By ea11
Thanks for the reply. I though cutadapt did that...

Thanks for the reply. I though cutadapt did that with the -p option to specify paired end data.
I shall give BBDuk a try and see the results. I was not happy with the results of trimmomatic on my...
Forum: Bioinformatics 11-06-2015, 12:31 AM
Replies: 6
Views: 2,411
Posted By ea11
Tophat2 high discordant alignments

Hi,

I am mapping paired end RNAseq data using tophat2, but the alignment summary generated is showing I am getting a very high discordant alignment rate. The only tophat options I am specifying is...
Forum: Bioinformatics 11-05-2015, 01:55 AM
Replies: 0
Views: 983
Posted By ea11
Showing results 1 to 25 of 36

 


All times are GMT -8. The time now is 10:40 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO