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Forum: Bioinformatics 02-06-2018, 11:05 AM
Replies: 3
Views: 2,841
Posted By Fad2012
Bandana: ViReMa will find insertion regardless of...

Bandana: ViReMa will find insertion regardless of their size, you can find out by subtracting the start and end location.

Gringer: You need to have your own control to study the sensitivity and...
Forum: Bioinformatics 07-12-2017, 03:27 PM
Replies: 12
Views: 1,323
Posted By Fad2012
Thank you

I really appreciate your help, I will play around with it and will let you know

Many thanks
Fadi
Forum: Bioinformatics 07-12-2017, 03:15 PM
Replies: 12
Views: 1,323
Posted By Fad2012
Well, when I replaced the "eq" with "=~" things...

Well, when I replaced the "eq" with "=~" things worked and it printed:
in if statement
in if statement

It seems that the eq is not working
Forum: Bioinformatics 07-12-2017, 03:06 PM
Replies: 12
Views: 1,323
Posted By Fad2012
Nothing appeared, so that means the statement is...

Nothing appeared, so that means the statement is not working?
Forum: Bioinformatics 07-12-2017, 02:27 PM
Replies: 12
Views: 1,323
Posted By Fad2012
Thank you very much SNPsaurus. I removed...

Thank you very much SNPsaurus.

I removed the column titles for now. So I removed the ID nad the Kind from the table. WhenI use print "f0 $fields[0]\tf1 $fields[1]\n"; It prints the following

...
Forum: Bioinformatics 07-12-2017, 02:09 PM
Replies: 12
Views: 1,323
Posted By Fad2012
Hi SNPsaurus Yes, I tried. The only way it...

Hi SNPsaurus

Yes, I tried. The only way it printed something when I put

print "fields[0] \n"

Just after the split command. I tried to play with many other things with no positive results....
Forum: Bioinformatics 07-11-2017, 02:46 PM
Replies: 12
Views: 1,323
Posted By Fad2012
Thank you SNPsaurus. I am not sure what is going...

Thank you SNPsaurus. I am not sure what is going on with this code.
Any suggestion anyone
Many thanks
Forum: Bioinformatics 07-06-2017, 11:48 AM
Replies: 12
Views: 1,323
Posted By Fad2012
PS. The code is printing nothing upon execution!

PS.
The code is printing nothing upon execution!
Forum: Bioinformatics 07-06-2017, 11:42 AM
Replies: 12
Views: 1,323
Posted By Fad2012
Need help with Perl

Hello guys

I have the following dataset

ID Kind
259 P0_P2
260 P0_P2
57 P2
58 P2
59 P2
Forum: Bioinformatics 01-01-2016, 07:16 AM
Replies: 2
Views: 1,251
Posted By Fad2012
Thank you fanli, I appreciate your suggestion. ...

Thank you fanli, I appreciate your suggestion.

I am in the final stage of my research:eek:, and wanted to look around if there is any ready code that can help me, so I can save myself some time...
Forum: Bioinformatics 12-30-2015, 07:27 AM
Replies: 2
Views: 1,251
Posted By Fad2012
Extract several DNA ranges from reference sequence. (need help)

Hello everybody

I am trying to find a ready Perl scrip, or any equivalent solution, to help me my data analysis task.

I need a code that takes a CVS file contains DNA ranges, and extract them...
Forum: Bioinformatics 11-22-2015, 03:35 PM
Replies: 6
Views: 1,609
Posted By Fad2012
Many thanks

Many thanks
Forum: Bioinformatics 11-22-2015, 08:15 AM
Replies: 6
Views: 1,609
Posted By Fad2012
Thanks very much Brian, could you please tell me...

Thanks very much Brian, could you please tell me a key though of how this can be done? Do I have to find first the actual coverage for one point, and use it as a reference? Or I can use the coverage...
Forum: Bioinformatics 11-22-2015, 04:48 AM
Replies: 6
Views: 1,609
Posted By Fad2012
mmmm I see..yes this is the plan, to shear the...

mmmm I see..yes this is the plan, to shear the amplicon.

What If I use a simulated data, that is perfectly normally distributed, can I use this average coverage to calculate a specific point...
Forum: Bioinformatics 11-21-2015, 11:48 AM
Replies: 6
Views: 1,609
Posted By Fad2012
specific location coverage from average coverage?

Hello there,

I want to know if there is any way to calculate the coverage at a specific nucleotide across the amplicon using the average coverage, with the assumption that the reads are normally...
Forum: Illumina/Solexa 10-30-2015, 03:13 AM
Replies: 4
Views: 2,914
Posted By Fad2012
Just copy the following and save it as .mconf,...

Just copy the following and save it as .mconf, and you can use it (300nts, 1%error):


(A,C) 0.3177499213
(A,T) 0.2331013755
(A,G) 0.4491487033

(C,A) 0.348955033
(C,T) 0.4592411105
(C,G)...
Forum: Sample Prep / Library Generation 10-23-2015, 04:08 AM
Replies: 3
Views: 8,810
Posted By Fad2012
Hello guys If the fragmentation is...

Hello guys

If the fragmentation is following a normal distribution, shouldn't the ends be underrepresented (less coverage or the rest of the amplicon). But what is appearing in this paper is the...
Forum: Pacific Biosciences 05-01-2015, 02:07 AM
Replies: 2
Views: 2,691
Posted By Fad2012
Hi Tyson, I thought the 3 passes will...

Hi Tyson,

I thought the 3 passes will provide enough data for building the correcting the sequencing error. However, it seems that I did not take into consideration the new sequencing chemistry....
Forum: Pacific Biosciences 04-30-2015, 03:33 AM
Replies: 7
Views: 2,355
Posted By Fad2012
My concern is that we are taking a risk here, as...

My concern is that we are taking a risk here, as we are relying on the leaking-through 7.5kb molecules from the >6Kb molecules. I was wondering, by using the protocol you suggested, is it possible...
Forum: Pacific Biosciences 04-23-2015, 06:05 AM
Replies: 7
Views: 2,355
Posted By Fad2012
Hi rhall Thank you very much for your...

Hi rhall

Thank you very much for your informative response. I found from a webinar on 11th of February that PacBio can reach to 10kb (photo...
Forum: Pacific Biosciences 04-20-2015, 11:40 PM
Replies: 7
Views: 2,355
Posted By Fad2012
Thank you very much rhall. This is great, so...

Thank you very much rhall.

This is great, so the size selection is based on RNA classes. The protocol you mentioned is showing the size selection for maximum 6kb, is it also possible to do it for...
Forum: Pacific Biosciences 04-18-2015, 03:59 AM
Replies: 7
Views: 2,355
Posted By Fad2012
ISO-seq library preparation, is it size selection RNA classes or RNA fragments?

Dear all

I am preparing to do PacBio ISO-Seq sequencing for total RNA of HeLa cells infected with 7.5Kb virus, I am interested in the Viral transcripts. My question is about library preparation...
Forum: Pacific Biosciences 01-30-2015, 02:55 PM
Replies: 2
Views: 2,691
Posted By Fad2012
Targeted transcript sequencing-Iso-Seq

Hello guys,

Hi Guys,

I am preparing to use PacBio Isoforms sequencing, to sequence the total human RNA searching for specific transcripts, which are 7.4-7.7kb long, and occurring in a very...
Forum: Pacific Biosciences 01-27-2015, 05:09 AM
Replies: 5
Views: 2,390
Posted By Fad2012
Thank you very much :)

Thank you very much :)
Forum: Pacific Biosciences 01-22-2015, 01:23 PM
Replies: 5
Views: 2,390
Posted By Fad2012
Reference

Dear Brian, thank you for your answer.

Are you aware about any possible reference where I can find more detailed information about the process of producing forward and reverse reads, and how this...
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