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Search: Posts Made By: KnowNothing2
Forum: Bioinformatics 12-19-2013, 08:27 AM
Replies: 1
Views: 1,081
Posted By KnowNothing2
Good program for grouping genes/proteins

I have some RNAseq data that I would like to have grouped into protein families. I'm not exactly looking for a particular grouping at the moment, so any program would do.
Forum: Bioinformatics 12-11-2013, 09:37 AM
Replies: 10
Views: 2,691
Posted By KnowNothing2
right, so now how would I go about determining...

right, so now how would I go about determining which gene the first 2 correspond to? theoretically, these should all be exonic.
Forum: Bioinformatics 12-11-2013, 09:28 AM
Replies: 10
Views: 2,691
Posted By KnowNothing2
Here are my first 3 reads. ...

Here are my first 3 reads.
...
Forum: Bioinformatics 12-11-2013, 09:12 AM
Replies: 10
Views: 2,691
Posted By KnowNothing2
So then why aren't there any gene specific...

So then why aren't there any gene specific idnetifiers with this genome alignment, when all other SAM examples I see outputed from bowtie 2 have these identifiers?
Forum: Bioinformatics 12-11-2013, 07:18 AM
Replies: 10
Views: 2,691
Posted By KnowNothing2
Aligned to UCSC genome using Bowtie2, how do I interpret QNAME in SAM file?

I get identifiers like M00830:112:000000000-A6EGB:1:1101:13084:1783.
Forum: Bioinformatics 12-10-2013, 12:29 PM
Replies: 11
Views: 3,855
Posted By KnowNothing2
Right, I'll have to figure out some of the...

Right, I'll have to figure out some of the details. Right now, I just have an idea what I want to perform, but no real idea how to execute. But I did just read through a tutorial that kind of went...
Forum: Bioinformatics 12-10-2013, 12:03 PM
Replies: 11
Views: 3,855
Posted By KnowNothing2
So that's basically exactly what I was looking...

So that's basically exactly what I was looking for. Thanks!
Forum: Bioinformatics 12-10-2013, 11:51 AM
Replies: 11
Views: 3,855
Posted By KnowNothing2
I'm actually trying to write in python. How do I...

I'm actually trying to write in python. How do I notate a certain variable in a sam file (I'm very new to python bioinformatics).
Forum: Bioinformatics 12-10-2013, 11:34 AM
Replies: 3
Views: 1,316
Posted By KnowNothing2
Makes sense; however, if I recall correctly I ran...

Makes sense; however, if I recall correctly I ran --sensitive-local a few days ago and I got a lower coverage than with --very-fast-local.
Forum: Bioinformatics 12-10-2013, 11:17 AM
Replies: 11
Views: 3,855
Posted By KnowNothing2
Basically to write a program

Basically to write a program
Forum: Bioinformatics 12-10-2013, 10:37 AM
Replies: 11
Views: 3,855
Posted By KnowNothing2
What linux spreadsheet program can you open .sam files in?

Tried opening it in libre office calc but the program just freezes
Forum: Bioinformatics 12-10-2013, 10:32 AM
Replies: 3
Views: 1,316
Posted By KnowNothing2
Bowtie 2 parameters, how does this make sense

When I run:

--very-fast-local -L 20 -N 1

I get ~70% coverage onto my genome

To make my conditions less stringent, I ran

-D 5 -R 1 -N 1 -L 15 -i S,1,2.00 (which is essentially...
Forum: RNA Sequencing 12-04-2013, 02:56 PM
Replies: 4
Views: 1,937
Posted By KnowNothing2
Awesome thanks, so then why didn't I get 100%...

Awesome thanks, so then why didn't I get 100% coverage with a 15 seed. How will a 20 seed perform more optimally?
Forum: RNA Sequencing 12-04-2013, 02:23 PM
Replies: 4
Views: 1,937
Posted By KnowNothing2
Bowtie 2 parameters, these should be generous correct?

I previously ran my fastq file with parameters I can't remember and it gave me ~82% coverage.

Today (2 months later), I attempted even a less stringent run using

--local --norc -N1 -L 15
...
Forum: Sample Prep / Library Generation 12-02-2013, 02:28 PM
Replies: 1
Views: 2,096
Posted By KnowNothing2
Variances in ribosomal coat (which may or may not...

Variances in ribosomal coat (which may or may not exist) may skew results
Forum: RNA Sequencing 12-02-2013, 02:26 PM
Replies: 0
Views: 947
Posted By KnowNothing2
Evaluate the read location in reference to the CDS

I cross-referenced my BAM file to an annotated genome and got ~80% coverage. Is there a way I can quickly evaluate the density of reads with respect to the read location on the transcript?
Forum: RNA Sequencing 10-18-2013, 06:17 PM
Replies: 0
Views: 1,402
Posted By KnowNothing2
Does these Cuffcompare results look okay

I aligned my RNAseq data to the mouse mm10 genome using Bowtie2. I then generated a GTF file using Cufflinks, and then used Cuffcompare to compare against an annotated mouse genome (from UCSC Table...
Forum: RNA Sequencing 10-18-2013, 04:28 PM
Replies: 0
Views: 1,263
Posted By KnowNothing2
What is the actually output of a Cufflinks GFT file?

I've aligned my RNAseq data to the mouse genome using bowtie2, but I guess that output doesn't account for abundance, correct? So then you need to use cufflinks to quantify? Do I have this correct?
Forum: RNA Sequencing 10-18-2013, 02:15 PM
Replies: 4
Views: 1,649
Posted By KnowNothing2
I had a question about that. Does bowtie2 throw...

I had a question about that. Does bowtie2 throw reads out if they overlap at a splice junction since you're referencing to a genome ?
Forum: Bioinformatics 10-18-2013, 01:06 PM
Replies: 8
Views: 2,044
Posted By KnowNothing2
Awesome, thanks. So I now see if my reads...

Awesome, thanks. So I now see if my reads represent an exon, which is very useful. Now to find out which gene that is, do I need to just manual search them?

Also, how did you find the GFF3 file?...
Forum: Bioinformatics 10-18-2013, 12:01 PM
Replies: 8
Views: 2,044
Posted By KnowNothing2
Not easy, indeed. The reason I switched to a...

Not easy, indeed.

The reason I switched to a new program is because I indexed my bam file this morning and used that as the consensus file in Tablet. Maybe I'm not using Tablet correctly, but I...
Forum: RNA Sequencing 10-18-2013, 11:25 AM
Replies: 4
Views: 1,649
Posted By KnowNothing2
sequenced transcriptome- how do I identify my transcripts

Aligned to mm10 using bowtie2, and converted to a sorted bam using samtools. How do I analyze my reads and what transcripts they correspond to
Forum: Bioinformatics 10-18-2013, 11:20 AM
Replies: 8
Views: 2,044
Posted By KnowNothing2
Basically I performed RNA sequencing with ~30mers...

Basically I performed RNA sequencing with ~30mers using MiSeq. Now I just want to determine what genes are being transcribed. So aligned my reads to the mouse mm10 genome using bowtie 2. This...
Forum: Bioinformatics 10-18-2013, 10:54 AM
Replies: 8
Views: 2,044
Posted By KnowNothing2
So I was able to find reads after all; however,...

So I was able to find reads after all; however, there was no annotation other than chromosome location. So I gave up on Tablet. Basically, I'm just trying to figure out my reads from RNAseq, so...
Forum: Bioinformatics 10-18-2013, 09:03 AM
Replies: 8
Views: 2,044
Posted By KnowNothing2
Help with Tablet

So I have reads I have aligned to the mouse mm10 genome using Bowtie 2. I created a .bam from the .sam file, which I then used to make a sorted.bam and an indexed.bam.bai. I loaded the sorted.bam...
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