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Search: Posts Made By: ajsn6c
Forum: General 09-10-2018, 12:47 PM
Replies: 0
Views: 1,538
Posted By ajsn6c
Liftover dog canFam3 to human hg19

Hi my question is relatively simple. I've converted dog coordinates to human using UCSC LiftOver. These are 200bp intergenic regions that are differentially methylated from normal dogs to cancer...
Forum: RNA Sequencing 02-26-2018, 10:59 AM
Replies: 0
Views: 1,692
Posted By ajsn6c
Tophat2 alignment problem

I ran this code using tophat (v2.1.0) to align reads (bowtie2 (v2.2.6.0)) from my RNA-seq fastq file using the bowtie2 genomes.bt2 indexes from igenomes (Homo_sapiens_UCSC_hg19)(:

tophat2 -p 8 -G...
Forum: Sample Prep / Library Generation 07-21-2016, 01:57 PM
Replies: 1
Views: 903
Posted By ajsn6c
ChIP-seq and Peak calling

I have a simple question that I would like some opinions on. If a transcription factor is highly expressed (protein) in one cell and say now that the expression of is halved because of knock down...
Forum: Bioinformatics 06-20-2016, 09:47 AM
Replies: 0
Views: 1,275
Posted By ajsn6c
CummeRbund, extracting only one chromosome

So I'm new to R and want to create a scatterplot with cummeRbund that has only chr8 plots.

>pdf(file="practice_8.pdf")
> csScatter(genes(cuff_data), 'S1', 'S2')
> dev.off()

I feel like...
Forum: Bioinformatics 01-28-2016, 09:00 AM
Replies: 0
Views: 971
Posted By ajsn6c
MEDIPS by Lukas Chavez in R

I'm running a few quality controls using the most up to date MEDIPS package on my MacBook Air OS X El Capitan with 4GB of memory. I'm able to run the other quality controls: saturation analysis and...
Forum: Bioinformatics 10-20-2015, 04:12 PM
Replies: 2
Views: 1,293
Posted By ajsn6c
That makes sense, it talks about adding the GTF...

That makes sense, it talks about adding the GTF file statement at the end. Ill try it out! Thanks!
Forum: Bioinformatics 10-20-2015, 07:57 AM
Replies: 2
Views: 1,293
Posted By ajsn6c
Annotating dog coordinates using HOMER

So I have a bed file with dog genomic coordinates e.g. chr38 1232122 123555

I would like to use HOMER to annotate this. I use HOMER to annotate human peaks using the command:
...
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