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Forum: Epigenetics 12-24-2015, 12:11 AM
Replies: 1
Views: 2,127
Posted By Ohad
In my humble opinion, it is not mandatory. Though...

In my humble opinion, it is not mandatory. Though I guess it depends on what protein you precipitate.

Paired-end gives you the complete fragment location and therefore, you can adjust your...
Forum: Sample Prep / Library Generation 06-22-2015, 08:34 AM
Replies: 0
Views: 607
Posted By Ohad
cross-linking and sonication

Hi all,

Hope someone can help me with some issue the bothers me.
I was told that sonication usually does not shear DNA that is strongly bound by some protein due to previous cross-linking.
...
Forum: General 06-21-2015, 04:14 AM
Replies: 0
Views: 1,077
Posted By Ohad
ucsc custom track

Hi,

I want to load my bigwig file to view on ucsc.
I tried dropbox but I get the msg:



I think the problem is the lack of the 'url=<external_url>' parameter in my header track line.
...
Forum: Bioinformatics 07-30-2014, 05:28 AM
Replies: 2
Views: 1,367
Posted By Ohad
Can anyone offer an idea ?

Can anyone offer an idea ?
Forum: Bioinformatics 07-29-2014, 04:20 AM
Replies: 2
Views: 1,367
Posted By Ohad
I`m working too these days on ChIP data using...

I`m working too these days on ChIP data using HOMER and I encountered a related problem.

HOMER preform Basic Quality Analysis (attached) when executing makeTagDirectory which produces...
Forum: RNA Sequencing 06-10-2014, 05:59 AM
Replies: 6
Views: 2,417
Posted By Ohad
ok thank you for this help. I do have...

ok thank you for this help.

I do have paired-end reads, but I guess I could write some script to handle that, using the reads ID.

Nevertheless, I do preform differential exons analysis quite...
Forum: RNA Sequencing 06-10-2014, 05:45 AM
Replies: 6
Views: 2,417
Posted By Ohad
As for now I only need the expression, will...

As for now I only need the expression, will samtools be enough ?
I would like to save the time of learning how to use this package as I'm not that familiar yet with R
Forum: RNA Sequencing 06-10-2014, 05:28 AM
Replies: 6
Views: 2,417
Posted By Ohad
Do I need to install the whole package or can I...

Do I need to install the whole package or can I just use this one script ?
Forum: RNA Sequencing 06-10-2014, 05:14 AM
Replies: 6
Views: 2,417
Posted By Ohad
exon expression level

Hi there.

I would like to to get for a list of exons their expression level from my RNA-seq data.
I thought about using cufflinks but the problem is that cufflinks generate FPKM at the isoform...
Forum: Bioinformatics 05-11-2014, 02:03 AM
Replies: 8
Views: 1,755
Posted By Ohad
You need to take a look at your log file. I think...

You need to take a look at your log file. I think run.log
Also , what do you mean by "halts" ? are you sure it's not running ? does it crash at all ?
You are using -p 1 , why ? you have many...
Forum: Bioinformatics 05-10-2014, 02:33 AM
Replies: 8
Views: 1,755
Posted By Ohad
I would give a look at that file -...

I would give a look at that file - right_kept_reads_seg2
Check if it was created at all.
Forum: Bioinformatics 05-09-2014, 07:11 AM
Replies: 14
Views: 3,190
Posted By Ohad
For my taste your distribution looks fine, and I...

For my taste your distribution looks fine, and I think that an avg of 170 is fine as well.
I don't understand why novel transcripts are suspicious to you regarding fragment distribution.

I...
Forum: Bioinformatics 05-09-2014, 05:35 AM
Replies: 14
Views: 3,190
Posted By Ohad
* What I meant was --no-length-correction should...

* What I meant was --no-length-correction should be used WHEN no fragmentation was done. Sorry for the confusion

NOObseq, you should add the reads lengths of both mates themselves to that -30 and...
Forum: Bioinformatics 05-09-2014, 04:26 AM
Replies: 14
Views: 3,190
Posted By Ohad
For what I understand --no-length-correction is...

For what I understand --no-length-correction is just the FPM out of FPKM

If no fragmentation was done, no need to add the per Kilo-base
Forum: Bioinformatics 05-09-2014, 03:56 AM
Replies: 14
Views: 3,190
Posted By Ohad
Oh my :) I think you both won the discussion...

Oh my :)

I think you both won the discussion :)

I guess everyone agrees this values are just to say - be aware that those Mirs are highly expressed, but don't assume the numbers are reliable.
...
Forum: Bioinformatics 05-09-2014, 03:25 AM
Replies: 3
Views: 1,922
Posted By Ohad
I downloaded ref_Amel_4.5_scaffolds.gff3 And...

I downloaded ref_Amel_4.5_scaffolds.gff3

And I see XM_006557348.1, XM_001122629.3 and XM_006557349.1 inside...
Forum: Bioinformatics 05-09-2014, 03:09 AM
Replies: 14
Views: 3,190
Posted By Ohad
That is what I mean I wanted to know those...

That is what I mean

I wanted to know those values represent a true expression, as it is the first time I get such high values on RNA-seq

I was worried they might be contamination of some sort...
Forum: Bioinformatics 05-09-2014, 03:00 AM
Replies: 2
Views: 1,143
Posted By Ohad
I think this is your prolem: -x...

I think this is your prolem:

-x /home/Hg19/Reference/humanGenome

Are your files named "humanGenome.1.rev.bt2 ..etc" ?

I think you should use:

-x /home/Hg19/Reference/humanGenome/hg19 if...
Forum: Bioinformatics 05-09-2014, 02:55 AM
Replies: 14
Views: 3,190
Posted By Ohad
Thanks But are those values represent a good...

Thanks

But are those values represent a good value ?
Forum: Bioinformatics 05-08-2014, 04:59 AM
Replies: 14
Views: 3,190
Posted By Ohad
High values of FPKM on cuffdiff

Hi all,

I run cuffdiff on my control vs condition to check if the mRNA expression of the gene I've knocked-down (from Hela cells) is lower than the mRNA expression of my control.

Gladly I saw...
Forum: General 03-02-2014, 03:52 PM
Replies: 2
Views: 1,798
Posted By Ohad
I just finished doing fastqc. I see most reads...

I just finished doing fastqc.
I see most reads are 50bp, but there are 40 and 36 as well.
Quality control is GREEN and the box-plot way of distribution shows a large amount of reads with the...
Forum: General 03-02-2014, 09:48 AM
Replies: 2
Views: 1,798
Posted By Ohad
Cleaning MNase BAM file

Hi,
I have this dataset of MNase.
the raw reads were aligned with bwa, the BAM file is about 60GB, and I wonder if I should filter it.

The header of the file looks like this:
...
Forum: Illumina/Solexa 08-06-2013, 08:31 AM
Replies: 8
Views: 2,068
Posted By Ohad
Thank you both for your wise suggestions.

Thank you both for your wise suggestions.
Forum: Illumina/Solexa 08-06-2013, 08:23 AM
Replies: 8
Views: 2,068
Posted By Ohad
Thank you felix. I assume you suggest that...

Thank you felix.

I assume you suggest that since TG will cut all remaining bases downstream to the 13bp adapter matched anyhow (if they ever exist on a particular read, and probably containing...
Forum: Illumina/Solexa 08-06-2013, 05:30 AM
Replies: 8
Views: 2,068
Posted By Ohad
I read more about multiplexed sequencing with PE ...

I read more about multiplexed sequencing with PE

So, for adapters trimming I assume I need to trim Adapter #1 as is ,and one of the other adapters (depends on the file im working on) when it's...
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