Forum: Bioinformatics
09-16-2016, 12:14 PM
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Replies: 0
Views: 1,188
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...
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Forum: Bioinformatics
09-03-2016, 03:49 PM
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Replies: 5
Views: 2,048
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....
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Forum: Bioinformatics
08-30-2016, 08:39 PM
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Replies: 5
Views: 2,048
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...
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Forum: Bioinformatics
08-30-2016, 05:41 PM
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Replies: 5
Views: 2,048
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...
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Forum: RNA Sequencing
10-07-2015, 05:18 PM
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Replies: 3
Views: 2,091
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Forum: General
03-06-2015, 10:28 AM
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Replies: 2
Views: 1,258
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...
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Forum: Bioinformatics
03-06-2015, 10:11 AM
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Replies: 1
Views: 906
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...
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Forum: Bioinformatics
03-14-2014, 06:21 PM
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Replies: 10
Views: 3,921
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...
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Forum: Bioinformatics
03-14-2014, 12:41 PM
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Replies: 10
Views: 3,921
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...
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Forum: Bioinformatics
10-27-2013, 03:47 PM
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Replies: 2
Views: 1,217
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...
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Forum: Bioinformatics
04-26-2013, 05:37 PM
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Replies: 4
Views: 3,567
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Forum: RNA Sequencing
02-13-2013, 02:13 PM
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Replies: 11
Views: 10,718
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Forum: General
08-11-2012, 03:58 PM
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Replies: 2
Views: 2,150
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Forum: General
08-08-2012, 03:04 PM
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Replies: 2
Views: 2,150
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...
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Forum: General
08-06-2012, 01:35 PM
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Replies: 2
Views: 2,803
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...
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Forum: Introductions
07-16-2012, 04:03 PM
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Replies: 3
Views: 2,853
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Forum: Introductions
07-15-2012, 01:02 PM
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Replies: 3
Views: 2,853
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Forum: Bioinformatics
05-11-2012, 10:15 AM
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Replies: 2
Views: 1,217
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...
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Forum: Bioinformatics
07-26-2011, 10:29 AM
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Replies: 3
Views: 1,562
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...
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Forum: Bioinformatics
07-25-2011, 02:22 PM
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Replies: 3
Views: 1,562
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),...
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Forum: Bioinformatics
07-25-2011, 12:04 PM
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Replies: 3
Views: 3,833
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.
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Forum: Bioinformatics
07-25-2011, 10:29 AM
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Replies: 4
Views: 6,871
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Forum: Bioinformatics
07-21-2011, 02:15 PM
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Replies: 7
Views: 1,843
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Forum: Bioinformatics
07-19-2011, 06:20 PM
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Replies: 5
Views: 3,174
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...
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Forum: Bioinformatics
07-19-2011, 01:56 PM
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Replies: 3
Views: 3,981
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