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Search: Posts Made By: Milestailsprowe
Forum: Bioinformatics 11-03-2015, 01:04 PM
Replies: 24
Views: 3,040
Posted By Milestailsprowe
Oh. I have one file that I got to work in...

Oh. I have one file that I got to work in goldenhelix. I just compare it to the the one I showed you and there is a big difference in the %. What does that mean
http://i.imgur.com/huXGsRX.png
Forum: Bioinformatics 11-03-2015, 11:14 AM
Replies: 24
Views: 3,040
Posted By Milestailsprowe
What does it mean http://i.imgur.com/WkKCmC7.png

What does it mean
http://i.imgur.com/WkKCmC7.png
Forum: Bioinformatics 11-03-2015, 10:29 AM
Replies: 24
Views: 3,040
Posted By Milestailsprowe
I'm usuing version 2.3.14 (16) Can you...

I'm usuing version 2.3.14 (16)

Can you please give me a run down on how you would do it from start the finish. NOthing is showing up

Where would you download your orginal file? Please. dont...
Forum: Bioinformatics 11-02-2015, 06:10 PM
Replies: 24
Views: 3,040
Posted By Milestailsprowe
Didnt work ...

Didnt work



http://i.imgur.com/oWdmSAN.png

Where do I put the .gtf file?

Thank you for all your help. I'm a graduate student trying to figure this out and my professor never has time sadly
Forum: Bioinformatics 11-02-2015, 02:58 PM
Replies: 24
Views: 3,040
Posted By Milestailsprowe
I downloaded the NCBI GRCm38 version. Should I...

I downloaded the NCBI GRCm38 version. Should I use something else? Which one would you use?
Forum: Bioinformatics 11-02-2015, 01:57 PM
Replies: 24
Views: 3,040
Posted By Milestailsprowe
Thanks for the help. I got the reference one from...

Thanks for the help. I got the reference one from igenome. Trying to get this mouse data to show.

http://i.imgur.com/oJ7DSyE.png
Forum: Bioinformatics 11-02-2015, 12:40 PM
Replies: 24
Views: 3,040
Posted By Milestailsprowe
Went all the way and didnt see anything. Nothing...

Went all the way and didnt see anything. Nothing is showing up
Forum: Bioinformatics 11-02-2015, 11:19 AM
Replies: 24
Views: 3,040
Posted By Milestailsprowe
gave it a run with a mouse genome and .bam. Got...

gave it a run with a mouse genome and .bam. Got this

http://i.imgur.com/a0Jkfrd.png

As you can see the file is over a gigabyte so there is data in there
Forum: Bioinformatics 11-01-2015, 10:19 PM
Replies: 24
Views: 3,040
Posted By Milestailsprowe
Considering my current method can you give me a...

Considering my current method can you give me a quick run down on how to insert it into IGV. I'm not getting anything.

What is the process from fasta or fastq or whatever format to IGV
Forum: Bioinformatics 10-29-2015, 09:59 PM
Replies: 24
Views: 3,040
Posted By Milestailsprowe
I want to compare things in the liver over...

I want to compare things in the liver over multiple SRAs and I will try to sort it and report back
Forum: Bioinformatics 10-29-2015, 01:07 PM
Replies: 24
Views: 3,040
Posted By Milestailsprowe
Getting data into Golden Helix Genome Broswer

Hello I'm trying to get my sorted bam files to read into golden helixs genome broswer. I'm currently using version 2.1.0. Alot of my data comes into the broswer as Did not successfully write coverage...
Forum: Bioinformatics 08-31-2015, 01:02 PM
Replies: 5
Views: 833
Posted By Milestailsprowe
I got it to work doing that with Bowtie2-Align...

I got it to work doing that with Bowtie2-Align before it would say Bowtie2 exited at value 1. I got the Mouse one to to work from Igenome but now a set I've done Bowtie2-Build on before is giving me...
Forum: Bioinformatics 08-30-2015, 04:00 PM
Replies: 5
Views: 833
Posted By Milestailsprowe
I retried bowtie2-build on a set I've gotten it...

I retried bowtie2-build on a set I've gotten it to work and gor Total time for backward call to driver() for mirror index:1:31:06

All I did was

bowtie2-build (name of the index) and then (what...
Forum: Bioinformatics 08-29-2015, 08:12 PM
Replies: 5
Views: 833
Posted By Milestailsprowe
Bowtie2 Issue:Backward call to driver()

Hello everyone I'm trying to use bowtie2-build and keep getting backward call to driver for mirror index issue.

I'm not sure what the issue is

I'm using

bowtie2-build -f genome.fa...
Forum: Bioinformatics 08-12-2015, 09:43 AM
Replies: 4
Views: 1,243
Posted By Milestailsprowe
Ok I will index the file and trying Bowtie 2...

Ok I will index the file and trying Bowtie 2 Large option
Forum: Bioinformatics 08-12-2015, 09:18 AM
Replies: 4
Views: 1,243
Posted By Milestailsprowe
Fastq file too big for Bowtie2?

Hello I'm trying to use Bowtie2-Build on the Pig Fastq SRR689228.fastq. I'm getting a error sayings its the file is too big.

http://i.imgur.com/zZKga7L.jpg

How can I fix this problem?
Forum: Bioinformatics 07-18-2015, 10:30 AM
Replies: 4
Views: 1,183
Posted By Milestailsprowe
So do I sort the bam files using @HD VN:1.0 ...

So do I sort the bam files using @HD VN:1.0 SO:coordinate with samtools?
Forum: Bioinformatics 07-18-2015, 09:12 AM
Replies: 4
Views: 1,183
Posted By Milestailsprowe
Cuffdiff issue: Sort order of reads in BAMS must be the same

Hello. I'm having issues with Cuffdiff and can not figure out why. The program says the read order has to be the same but I ran all of then with Samtools sort -n to make sure and still having that...
Forum: Bioinformatics 07-09-2015, 05:33 AM
Replies: 3
Views: 2,157
Posted By Milestailsprowe
So... If I have two transcript.gtf files I use...

So... If I have two transcript.gtf files I use what command? Just more assemblies.txt?
Forum: Bioinformatics 07-09-2015, 12:36 AM
Replies: 3
Views: 2,157
Posted By Milestailsprowe
How do I merge .gtf files

Hello. I'm trying to merge transcript.gtf I got from using cufflinks. Can someone explain how to make the assemblies.txt file
Forum: Bioinformatics 06-23-2015, 02:36 PM
Replies: 8
Views: 979
Posted By Milestailsprowe
Well ok so thats helps the situation. All data...

Well ok so thats helps the situation. All data must be aligned through tophat then
Forum: Bioinformatics 06-23-2015, 01:47 PM
Replies: 8
Views: 979
Posted By Milestailsprowe
So I cant use anything from bowtie in tophat. The...

So I cant use anything from bowtie in tophat. The data is from bowtie2-align
Forum: Bioinformatics 06-23-2015, 01:30 PM
Replies: 8
Views: 979
Posted By Milestailsprowe
So how would I prepare them for cuffdiff? Sorry...

So how would I prepare them for cuffdiff? Sorry if I come off uninformed I'm doing all this for my thesis project
Forum: Bioinformatics 06-23-2015, 12:54 PM
Replies: 8
Views: 979
Posted By Milestailsprowe
Convert Bowtie2 alignments into Bam files.

Hello I have alot of bowtie2 data in plaintext files. What would be the easist way to convert that data into .bam files for tophat/cuffdiff
Forum: Bioinformatics 06-10-2015, 07:06 PM
Replies: 14
Views: 7,148
Posted By Milestailsprowe
Fixed the wrong command

Fixed the wrong command
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