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Forum: Sample Prep / Library Generation 03-11-2015, 03:52 PM
Replies: 5
Views: 1,575
Posted By SeqVicious
Also, I should note that I have the sequencing...

Also, I should note that I have the sequencing center at my university do the bioanalyzer. I can try asking them if I can get the data in a different format.
Forum: Sample Prep / Library Generation 03-11-2015, 03:51 PM
Replies: 5
Views: 1,575
Posted By SeqVicious
Why does this seem overloaded? It's only 20ng/ul....

Why does this seem overloaded? It's only 20ng/ul. How do I select a range? Can I do this in the actual data on the computer software?
Forum: Sample Prep / Library Generation 03-11-2015, 11:33 AM
Replies: 5
Views: 1,575
Posted By SeqVicious
mRNA pico - Can't determine exact RNA size

Hi all,

I'm performing an altered RNAseq library preparation where I need to start from between 80 and 110 bp of fragmented mRNA. I ran the samples on a Urea-PAGE gel and extracted my sizes. I ran...
Forum: Sample Prep / Library Generation 01-05-2015, 03:20 PM
Replies: 4
Views: 2,797
Posted By SeqVicious
Thank you for the responses. I will trust my RNA...

Thank you for the responses. I will trust my RNA based on the rRNA peaks and continue on!
Forum: Sample Prep / Library Generation 12-11-2014, 01:05 PM
Replies: 4
Views: 2,797
Posted By SeqVicious
Good RIN, bad mRNA?

Hello, I'm preparing some RNA for RNAseq and I submitted my samples to the local sequencing core for quality control on the bioanalyzer. The results came back and my samples have good RIN values,...
Forum: Bioinformatics 08-08-2012, 11:47 AM
Replies: 5
Views: 2,726
Posted By SeqVicious
Thank you. I am going to give GATK a try. Luckily...

Thank you. I am going to give GATK a try. Luckily I already have this installed.

Cheers.
Forum: Bioinformatics 08-08-2012, 09:35 AM
Replies: 5
Views: 2,726
Posted By SeqVicious
How do calculate % of genome with >20x coverage?

Hi all,

I've searched through the forums for my question but I haven't found anything for my specific stat that I'm looking for. How do you figure out the % of your genome that had >20x coverage?...
Forum: Bioinformatics 01-28-2012, 10:53 AM
Replies: 6
Views: 5,329
Posted By SeqVicious
Thank you for your help guys, I got it to work.

Thank you for your help guys, I got it to work.
Forum: Bioinformatics 01-28-2012, 06:29 AM
Replies: 6
Views: 5,329
Posted By SeqVicious
When I try to load a .bam file it tells me it...

When I try to load a .bam file it tells me it needs to be indexed. Do I have to load both the .bam and the index simultaneously?
Forum: Bioinformatics 01-27-2012, 02:12 PM
Replies: 6
Views: 5,329
Posted By SeqVicious
Bam indexing problem?

After a struggle to get samtools successfully installed and working on my windows machine, I'm now having trouble (I think) indexing a bam file. I'm using cygwin to use samtools. I'm planning on...
Forum: Bioinformatics 01-27-2012, 01:32 PM
Replies: 24
Views: 19,326
Posted By SeqVicious
Thank you for your help, it's all working now

Thank you for your help, it's all working now
Forum: Bioinformatics 01-27-2012, 01:15 PM
Replies: 24
Views: 19,326
Posted By SeqVicious
Thank you Richard Finney. I just made these...

Thank you Richard Finney. I just made these corrections and the make samtools command finished. Unfortunately, when I try to use samtools the samtools command cannot be found. Did something go wrong...
Forum: Bioinformatics 01-27-2012, 09:59 AM
Replies: 24
Views: 19,326
Posted By SeqVicious
Thanks for trying, Carlos. I found a fix...

Thanks for trying, Carlos.

I found a fix suggested on another post but I have no idea how to implement it. The fix is adding

CC= gcc
CFLAGS= -g -Wall -O2 #-m64 #-arch ppc
CFLAGS=...
Forum: Bioinformatics 01-27-2012, 09:36 AM
Replies: 24
Views: 19,326
Posted By SeqVicious
I installed anything with the name 'curses' in it...

I installed anything with the name 'curses' in it during the cygwin installation and I'm still getting the following right before termination.

gcc -c -g -Wall -O2 -D_FILE_BITS=64...
Forum: Bioinformatics 01-27-2012, 09:28 AM
Replies: 24
Views: 19,326
Posted By SeqVicious
I'm on windows 7 and I'm using cygwin. I just...

I'm on windows 7 and I'm using cygwin. I just installed zlib by updating cygwin and the command got much further. This time curses.h failed and the command was terminated. I'll try installing...
Forum: Bioinformatics 01-27-2012, 09:14 AM
Replies: 24
Views: 19,326
Posted By SeqVicious
Samtools installation

Hi all,

I'm very new to bioinformatics and all I'm trying to do is index a bam file so I can view the pileup in IGV. I've downloaded the latest version of samtools unpacked it successfully. I'm...
Forum: Bioinformatics 01-26-2012, 01:57 PM
Replies: 34
Views: 14,542
Posted By SeqVicious
Also, I have redownloaded and the same message...

Also, I have redownloaded and the same message shows up.
Forum: Bioinformatics 01-26-2012, 01:27 PM
Replies: 34
Views: 14,542
Posted By SeqVicious
I'm also having a problem installing samtools...

I'm also having a problem installing samtools under cygwin. after executing: tar xjvf <file location> I get the error of "Compressed file ends unexpectedly." It then proceeds to tell me that the file...
Forum: Illumina/Solexa 09-26-2011, 03:12 PM
Replies: 1
Views: 2,370
Posted By SeqVicious
Also, I've been trying to find these on my own...

Also, I've been trying to find these on my own but I guess I just don't know enough about this stuff yet. What are the SE and PE primers?
Forum: Illumina/Solexa 09-26-2011, 02:49 PM
Replies: 1
Views: 2,370
Posted By SeqVicious
Current read1, index, and read2 primers for HiSeq2000

Hi all,

I'm currently being thrown into creating a library prep for some samples in our lab. We plan on multiplexing because and we want to throw in upwards of 6 samples. My lab has created...
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