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Search: Posts Made By: Ajayi Oyeyemi
Forum: Bioinformatics 04-11-2013, 01:11 PM
Replies: 11
Views: 5,864
Posted By Ajayi Oyeyemi
and in addition to the above, can someone help me...

and in addition to the above, can someone help me with the cuffcompare output posted above to answer this questions:

Determining the total number of transcripts (Known, partial and novel) ...
Forum: Bioinformatics 04-11-2013, 12:56 PM
Replies: 11
Views: 5,864
Posted By Ajayi Oyeyemi
Can someone help me out with this cuffcompare...

Can someone help me out with this cuffcompare output.
I'm imploring someone to please help or provide a link that will give me more information.
Forum: Bioinformatics 04-09-2013, 06:40 AM
Replies: 24
Views: 3,323
Posted By Ajayi Oyeyemi
Thanks Simon. Given that I don't have much...

Thanks Simon.

Given that I don't have much experience with the fiddling strategy you proposed, I'll just stick to ensemble anyway. I used samtools to check counts for unique alignments and I just...
Forum: Bioinformatics 04-09-2013, 06:37 AM
Replies: 24
Views: 3,323
Posted By Ajayi Oyeyemi
@Darwin, Thanks for the advice. I followed...

@Darwin,

Thanks for the advice. I followed your lead and I use the following code:
samtools view -q 50 -c sample1.bam > sample_uniquehits.bam

count = 39647278

samtools view -q 1 -c...
Forum: Bioinformatics 04-05-2013, 09:05 AM
Replies: 24
Views: 3,323
Posted By Ajayi Oyeyemi
@Simon., I'll do some of the sequences and...

@Simon.,
I'll do some of the sequences and blast them as advised. However, a thorough inspection of my sam file revealed that there are some with NH:2, NH:4 NH:16 and NH:20. I guess that's the...
Forum: Bioinformatics 04-05-2013, 08:42 AM
Replies: 24
Views: 3,323
Posted By Ajayi Oyeyemi
Thanks Darwin and truthfully, it is a perfect...

Thanks Darwin and truthfully, it is a perfect storm indeed. I used fastX tools to clip and trim my sequences. The boxplots ranged from 30 to 40. The size of the pictures is more than what it can...
Forum: Bioinformatics 04-05-2013, 08:02 AM
Replies: 24
Views: 3,323
Posted By Ajayi Oyeyemi
Simon and all, I found another one(see the...

Simon and all,

I found another one(see the attached). I used cufflinks to assemble the transcripts and it appears that cufflinks assembled the reads in between these two genes as shown. I went...
Forum: Bioinformatics 04-05-2013, 07:35 AM
Replies: 24
Views: 3,323
Posted By Ajayi Oyeyemi
I clicked on the link that connects ensemble to...

I clicked on the link that connects ensemble to ucsc and ncbi. Interestingly in ncbi region 79,025,650-79,027,700 bp, version 6.1 in Mapview, there seems to be a gene lying in that region...
Forum: Bioinformatics 04-05-2013, 07:25 AM
Replies: 24
Views: 3,323
Posted By Ajayi Oyeyemi
HTSeq

@Simon,

I took a snapshot of one of the regions where I have huge reads mapping to it(in the repeat_igv_file). There isn't any gene lying in that region. I went to check in ensemble as advised and...
Forum: Bioinformatics 04-05-2013, 06:17 AM
Replies: 24
Views: 3,323
Posted By Ajayi Oyeyemi
@Darwin, Thanks Darwin. The Agilent readings...

@Darwin,
Thanks Darwin. The Agilent readings were between 6.8 and 7.4. We decided to give this a shot because the samples were so hard to get.

IS there anyway one can beat around this?
Forum: Bioinformatics 04-05-2013, 06:13 AM
Replies: 24
Views: 3,323
Posted By Ajayi Oyeyemi
Thanks Simon and all. I had a second look at the...

Thanks Simon and all. I had a second look at the alignment and I observed that while some aligned in the genes, it appears that vast majority of reads aligning to regions farther away from known...
Forum: Bioinformatics 04-04-2013, 07:08 AM
Replies: 24
Views: 3,323
Posted By Ajayi Oyeyemi
htseq

@Simon and All,

I investigated my bam files as advised by Simon and I was able to take some snap shots. Can you help me take a look? I could see some of my reads in the intergenic region with most...
Forum: Bioinformatics 04-03-2013, 11:05 AM
Replies: 24
Views: 3,323
Posted By Ajayi Oyeyemi
Thanks Simon; I have igv installed on my system....

Thanks Simon; I have igv installed on my system. What are the things to watch out for. How can I know if a read is mapping to multiple regions using the igv. I'm so sorry as I'm just a newbie...
Forum: Bioinformatics 04-03-2013, 11:02 AM
Replies: 24
Views: 3,323
Posted By Ajayi Oyeyemi
Sorry I'm a newbie. Can you be more explicit? How...

Sorry I'm a newbie. Can you be more explicit? How can I run HTSeq without the header of sam file? And how can it be removed?
I'm sorry if this question is naive.
Forum: Bioinformatics 04-01-2013, 05:44 PM
Replies: 24
Views: 3,323
Posted By Ajayi Oyeyemi
Hey Guys please help me. My question hasn't been...

Hey Guys please help me. My question hasn't been answered. Can someone help me out?
Forum: Bioinformatics 04-01-2013, 05:40 PM
Replies: 11
Views: 5,864
Posted By Ajayi Oyeyemi
Cuffcompare output

Hi Folks, I need your help on this isssue. I ran cuffcompare and I got the following output below:
#= Summary for dataset: cufflinks_6/transcripts.gtf :
# Query mRNAs : 41274 in 33119 loci ...
Forum: Bioinformatics 03-28-2013, 08:19 AM
Replies: 24
Views: 3,323
Posted By Ajayi Oyeyemi
HTseq help

Hi all,
I'm using htseq count and fortunately, I didn't get any error. However, what concerns me most is the no feature and the alignment not unique options. They've been given me headache. They are...
Forum: Bioinformatics 02-25-2013, 01:30 PM
Replies: 38
Views: 25,634
Posted By Ajayi Oyeyemi
Dario...You are awesome! Thanks, I've finally got...

Dario...You are awesome! Thanks, I've finally got it to work.
Forum: Bioinformatics 02-25-2013, 01:28 PM
Replies: 14
Views: 3,642
Posted By Ajayi Oyeyemi
Thanks Simon. I followed your que and it worked...

Thanks Simon. I followed your que and it worked for version 2.15. I'm using ubuntu linux and I tried to upgrade it to version 2.15.2 but it appears I couldn't figure it out. Is there anyone that...
Forum: Bioinformatics 02-22-2013, 11:50 AM
Replies: 14
Views: 3,642
Posted By Ajayi Oyeyemi
I was suspecting that it was incorrectly...

I was suspecting that it was incorrectly installed since I searched the package but couldn't get the script out. See a part of my ls -al for the script:

-rw-rw-r-- 1 imumorin imumorin 55209...
Forum: Bioinformatics 02-22-2013, 11:38 AM
Replies: 14
Views: 3,642
Posted By Ajayi Oyeyemi
Hi everyone, I've been trying to use the...

Hi everyone,
I've been trying to use the dexseq_prepare_annotation.py script but I kept on getting error. Please see the code below.

imumorin@ansci253135199:~/myrnaseqexp$ python...
Forum: Bioinformatics 02-18-2013, 03:41 PM
Replies: 38
Views: 25,634
Posted By Ajayi Oyeyemi
Thanks Dario. Did I get the soft-linking of the...

Thanks Dario. Did I get the soft-linking of the genes.gtf file? and is there a space between genome* and .(full stop sign). Sorry I'm a newbie...
Forum: Bioinformatics 02-18-2013, 12:18 PM
Replies: 38
Views: 25,634
Posted By Ajayi Oyeyemi
hanks Dario, let me be much more clearer. I...

hanks Dario, let me be much more clearer. I downloaded the cow genome from the igenome in cufflinks website and I unpacked the tar.gz file. I created a link using the ln -s function to the gtf file...
Forum: RNA Sequencing 02-15-2013, 06:37 AM
Replies: 2
Views: 1,683
Posted By Ajayi Oyeyemi
tophat alignment

Hi everyone,
I have multiple fastq files and I want to align them all at once to tophat. Is there any shortcut that could be adopted instead of mapping each reads one by one to tophat.

Thanks.
Forum: Bioinformatics 02-15-2013, 05:56 AM
Replies: 38
Views: 25,634
Posted By Ajayi Oyeyemi
index and gtf conflict.

Hi,
I downloaded the bovine genome from this site http://hgdownload.soe.ucsc.edu/goldenPath/bosTau7/bigZips/ and I used the bowtie2-build to construct my index files. However, my gtf file was also...
Showing results 1 to 25 of 30

 


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