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Forum: Bioinformatics 09-16-2016, 11:14 AM
Replies: 0
Views: 1,062
Posted By kwatts59
bcftools is printing <*> in the alt field

Hello everybody.
I am running bcftools on an mpileup file generated by samtools via the following command (I removed the paths and shortened the filenames for clarity):
samtools mpileup -E -uf...
Forum: Bioinformatics 09-03-2016, 02:49 PM
Replies: 5
Views: 1,708
Posted By kwatts59
Thanks for your help. I ran Memtest86 and just...

Thanks for your help.
I ran Memtest86 and just after a few seconds, the server rebooted. I took the server back to the electronics shop and they said the motherboard can't handle 20Gb of memory....
Forum: Bioinformatics 08-30-2016, 07:39 PM
Replies: 5
Views: 1,708
Posted By kwatts59
Thank you for your quick reply. I downloaded...

Thank you for your quick reply.
I downloaded the source code, unzipped it, and typed the "make" command without parameters to compile the source.
When I tried bowtie2-build program, it failed just...
Forum: Bioinformatics 08-30-2016, 04:41 PM
Replies: 5
Views: 1,708
Posted By kwatts59
bowtie2-build causing system crash

Hello everybody.
I hope somebody can help me.
I bought a new server a couple of days ago, a 6th generation i5 processor with 20Gb RAM.
I installed Fedora 24 and it appears to be fully functioning...
Forum: RNA Sequencing 10-07-2015, 04:18 PM
Replies: 3
Views: 1,866
Posted By kwatts59
Yes, I know this is an old post, but I reproduced...

Yes, I know this is an old post, but I reproduced the same problem.
I created a GFF file in Excel, transferred the file to the server and ran cuffdiff using the GFF file.
For me, the problem was...
Forum: General 03-06-2015, 09:28 AM
Replies: 2
Views: 1,058
Posted By kwatts59
I suggest writing a PERL script to convert the...

I suggest writing a PERL script to convert the data into the format you desire.
The alignment file looks very similar to Phylip format. Maybe you can just load it into Excel and manually modify it...
Forum: Bioinformatics 03-06-2015, 09:11 AM
Replies: 1
Views: 762
Posted By kwatts59
Downloading Genomes from the 1000 Genome Project

I was given the task of finding and downloading the entire assembled genomic sequence of 10 healthy humans (preferably male and of the same ethnic origin).
I went to the following FTP site...
Forum: Bioinformatics 03-14-2014, 05:21 PM
Replies: 10
Views: 3,484
Posted By kwatts59
Here is some additional info

Below is the run.log file:
/usr/local/bioinfo/cufflinks-2.1.1.Linux_x86_64/cuffmerge -o /rice2/cuffmerge4 /rice2/cuffmerge4/transcripts_gtf.list
gtf_to_sam -F...
Forum: Bioinformatics 03-14-2014, 11:41 AM
Replies: 10
Views: 3,484
Posted By kwatts59
Finding novel genes using Cufflinks/Cuffmerge

I am trying to identify novel genes from my RNA-seq data using Cufflinks. I ran Cufflinks on each of my bam files created by Tophat. Then I used Cuffmerge to combine the transcripts.gtf files...
Forum: Bioinformatics 10-27-2013, 02:47 PM
Replies: 2
Views: 1,023
Posted By kwatts59
To all, I discovered my problem with my RNA-seq...

To all,
I discovered my problem with my RNA-seq data. It looks like there was some rRNA contamination in my sample which accounted for 5% of the total reads in the sample. The rRNA genes are located...
Forum: Bioinformatics 04-26-2013, 04:37 PM
Replies: 4
Views: 3,214
Posted By kwatts59
How do you calculate standard deviation on replicate RNA-seq data?

To all,
I extracted RNA from 3 untreated samples and had RNA-seq analysis performed.
A couple months later, I extracted RNA from 3 treated samples and had RNA-seq analysis performed.

I ran...
Forum: RNA Sequencing 02-13-2013, 01:13 PM
Replies: 11
Views: 9,435
Posted By kwatts59
I had the same problem running Cufflinks v2.0 on...

I had the same problem running Cufflinks v2.0 on dmel release 5.49.
To get around the problem, I wrote a PERL script to pull out the lines from the GFF file containing the word "gene" in the third...
Forum: General 08-11-2012, 02:58 PM
Replies: 2
Views: 1,893
Posted By kwatts59
Thanks for your help. The third link was what I...

Thanks for your help. The third link was what I was looking for
http://hapmap.ncbi.nlm.nih.gov/biomart/
There are 26,291,752 known SNPs.
Forum: General 08-08-2012, 02:04 PM
Replies: 2
Views: 1,893
Posted By kwatts59
List of known human SNPs

Is here a website where I can download all the known SNPs of the human genome (version GRCh37/hg19) ?

I need to know the chromosome, the position, the reference nucleotide, the SNP nucleotide, the...
Forum: General 08-06-2012, 12:35 PM
Replies: 2
Views: 2,291
Posted By kwatts59
Is the geneom GRCh37/hg19 from a single person?

Sorry to ask such novice questions. :confused:
Is the GRCh37/hg19 genome the genome of a single individual, or the composite of multiple people?

What is the difference between GRCh37/hg19 and...
Forum: Introductions 07-16-2012, 03:03 PM
Replies: 3
Views: 2,559
Posted By kwatts59
Thanks Justin. SeattleSeq was exactly what I...

Thanks Justin. SeattleSeq was exactly what I needed.
Forum: Introductions 07-15-2012, 12:02 PM
Replies: 3
Views: 2,559
Posted By kwatts59
Finding amino acid from a position in the human genome

To all,
I have a database of SNPs and with the chromosome and location in the human genome.
For example, in human genome GRCh37/hg19, on Chromosome 1, position 1118275, in gene TTLL10, the...
Forum: Bioinformatics 05-11-2012, 09:15 AM
Replies: 2
Views: 1,023
Posted By kwatts59
More problems with Tophat (v1.3.2)

I ran tophat version 1.3.2 to align my deep sequencing data to my reference genome via the following command

tophat --solexa1.3-quals p 6 o /control/8905X1/tophat /rice_index/rice_index...
Forum: Bioinformatics 07-26-2011, 09:29 AM
Replies: 3
Views: 1,354
Posted By kwatts59
I think I figured it out. According to the...

I think I figured it out.
According to the paper, they performed 5 technical replicates on a brain sample.
That means they performed the RNA-seq library build and sequencing on the same brain...
Forum: Bioinformatics 07-25-2011, 01:22 PM
Replies: 3
Views: 1,354
Posted By kwatts59
Easy question from a noobie

Can someone please explain figure 2 "Scatterplots of Technical Replicates of Brain Sample" in the paper below?
The x and y axis are both labeled the same "Number of aligned reads (log scale),...
Forum: Bioinformatics 07-25-2011, 11:04 AM
Replies: 3
Views: 3,393
Posted By kwatts59
I found this link. ...

I found this link.

http://www.itefix.no/i2/node/11201

It may be that you have an old version of rsync.
Forum: Bioinformatics 07-25-2011, 09:29 AM
Replies: 4
Views: 6,612
Posted By kwatts59
I really need to know if this calculation is...

I really need to know if this calculation is correct or not.
Is there anybody out there that knows how to calculate RPKM?
Forum: Bioinformatics 07-21-2011, 01:15 PM
Replies: 7
Views: 1,568
Posted By kwatts59
Yes, here is the link to install UCSC genome...

Yes, here is the link to install UCSC genome browser
http://genome.ucsc.edu/admin/jk-install.html
Forum: Bioinformatics 07-19-2011, 05:20 PM
Replies: 5
Views: 2,621
Posted By kwatts59
I loaded all my short read data into an SQL...

I loaded all my short read data into an SQL database so that this information can be pulled out with a quick query.

For example, to find how many reads cover position 72342 of chr 1, just type in...
Forum: Bioinformatics 07-19-2011, 12:56 PM
Replies: 3
Views: 3,492
Posted By kwatts59
First find the number of reads that map at least...

First find the number of reads that map at least once. To do this, run bowtie with "-k 1" option. Lets call this number K1.

Then run bowtie with the "-k 2" option. This will report up to two...
Showing results 1 to 25 of 46

 


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