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Search: Posts Made By: mido1951
Forum: Bioinformatics 06-11-2017, 01:11 PM
Replies: 15
Views: 1,400
Posted By mido1951
Sorry but i had juste ~27000 reads not 2365043?? ...

Sorry but i had juste ~27000 reads not 2365043??
thank your for your response.
Forum: Bioinformatics 06-11-2017, 08:31 AM
Replies: 15
Views: 1,400
Posted By mido1951
ok. thank you for the link. I have one more...

ok. thank you for the link.
I have one more question to the output file of BBmap.
This is an output file:
Read 1 data: pct reads num reads pct bases num bases
...
Forum: Bioinformatics 06-08-2017, 11:44 PM
Replies: 15
Views: 1,400
Posted By mido1951
hello Brian, Can you explain me the algorithm...

hello Brian,
Can you explain me the algorithm of BBmap please?
Thanks
Forum: Bioinformatics 06-08-2017, 03:50 AM
Replies: 15
Views: 1,400
Posted By mido1951
I did a mapping of the long reads on a reference...

I did a mapping of the long reads on a reference genome using bbmap (with covstats option). I wanted to know if all the reference genome is covred by the long reads.

I do not mean what the...
Forum: Bioinformatics 06-08-2017, 02:04 AM
Replies: 15
Views: 1,400
Posted By mido1951
thank you for your response. Can you explain me...

thank you for your response.
Can you explain me this output please.

Average coverage: 25,49
Standard deviation: 6,38
Percent scaffolds with any coverage:...
Forum: Bioinformatics 06-07-2017, 06:59 AM
Replies: 15
Views: 1,400
Posted By mido1951
so BBmap do not do that? i must use BEDToos? ...

so BBmap do not do that?
i must use BEDToos?
Thanks
Forum: Bioinformatics 06-07-2017, 05:40 AM
Replies: 15
Views: 1,400
Posted By mido1951
BBMAP mapping tool

Hello,
I wanted to know if bbmap gives me the following informations because I have not found in the tool's description.
Does BBmap only give me statistics on the mapping of reads on the reference...
Forum: Pacific Biosciences 04-20-2017, 06:28 AM
Replies: 1
Views: 1,006
Posted By mido1951
Problem resolved

Problem resolved
Forum: Pacific Biosciences 04-20-2017, 04:12 AM
Replies: 1
Views: 1,006
Posted By mido1951
problem in PacBioToCA in correction of long reads

Hello,

I try to run PacBioToCA to correct long reads.

But here is the error.

can you help me
thanks
Forum: Bioinformatics 02-20-2016, 03:47 AM
Replies: 17
Views: 1,784
Posted By mido1951
for me, I want to express the error rate in the...

for me, I want to express the error rate in the equation.
From what I understood the error rate is equal: error rate = (S+I+D+N)/(M+S+I+D+N)
am i right?
then I want to see the distance used for...
Forum: Bioinformatics 02-19-2016, 12:33 PM
Replies: 17
Views: 1,784
Posted By mido1951
Is that the distance M=N=I=D=S=1?? any response...

Is that the distance M=N=I=D=S=1??
any response Brian?
Forum: Bioinformatics 02-19-2016, 06:00 AM
Replies: 17
Views: 1,784
Posted By mido1951
what's the distance used in every M, D, I,....??

what's the distance used in every M, D, I,....??
Forum: Bioinformatics 02-19-2016, 05:18 AM
Replies: 17
Views: 1,784
Posted By mido1951
the global error rate equation is: The error...

the global error rate equation is:
The error rate is (S+I+D+N)/(M+S+I+D+N) ??
Forum: Bioinformatics 02-19-2016, 04:33 AM
Replies: 17
Views: 1,784
Posted By mido1951
I did not use mapPacBio.sh because i have Minion...

I did not use mapPacBio.sh because i have Minion reads.
But I have corrected reads and I made a mapping these reads to the reference genome and I see the error rate.
but I have to express the error...
Forum: Bioinformatics 02-19-2016, 04:19 AM
Replies: 17
Views: 1,784
Posted By mido1951
thankyou Brian for your Explanations. I made a...

thankyou Brian for your Explanations.
I made a mapping with BBmap and i saw the error rate (% of bases with any errors) because you have told me the other day that we must take account of this error...
Forum: Bioinformatics 02-18-2016, 03:41 PM
Replies: 17
Views: 1,784
Posted By mido1951
no, I want to know how you get the error rate? ...

no, I want to know how you get the error rate?
what is the distance to get the error rate?
formally, how to express the error rate in BBMAP?

Error Rate: 23.1932% 281318 ...
Forum: Bioinformatics 02-18-2016, 02:58 PM
Replies: 17
Views: 1,784
Posted By mido1951
any response for this?

any response for this?
Forum: Bioinformatics 02-18-2016, 06:59 AM
Replies: 17
Views: 1,784
Posted By mido1951
Error rate in BBMAP

hello,
I want to know the equation error rate in BBMAP?
how you calcuer that rate?
Thank you for your reply.
@Brain?
Forum: Oxford Nanopore 01-30-2016, 05:36 AM
Replies: 2
Views: 2,855
Posted By mido1951
assembly "1D" or "2D" or "1D + 2D"

for assembling reads Minion.
Is it possible to use the reads "2D" + "1D" or only "2D"?
I mean is, we can try to put the "2D" and "1D" in a single file and try to do the assembly?
thanks for your...
Forum: Bioinformatics 01-30-2016, 04:12 AM
Replies: 2
Views: 702
Posted By mido1951
if i do an assembly of Short reads with Spades....

if i do an assembly of Short reads with Spades. So the time coplexity is O(n) where n is the number of short reads.(n>>>>m) "m is the number of K-mer".
can i consider this?
Thanks
Forum: Bioinformatics 01-29-2016, 02:17 PM
Replies: 2
Views: 702
Posted By mido1951
Complexity Time SPADES assembler

hello,
I want to know the time Complexity of Spades Assmbeler?
I did not find on the net. Can you help me?
and is this the complexity of blastn is O (mn) with m and n the lenght of the two...
Forum: Bioinformatics 01-23-2016, 09:01 AM
Replies: 10
Views: 1,140
Posted By mido1951
I used mapPacBio.sh and mapPacBio8k.sh. but the...

I used mapPacBio.sh and mapPacBio8k.sh.
but the execution takes a long time compared to bbmap.sh.
that's logic?
Forum: Bioinformatics 01-22-2016, 05:55 PM
Replies: 10
Views: 1,140
Posted By mido1951
i work with MinION reads with an average lenght...

i work with MinION reads with an average lenght ~5000bp.
For this i use mapPacBio.sh?

excuse me, for the error rate i work with "pct bases" column?
thanks
Forum: Bioinformatics 01-22-2016, 03:33 PM
Replies: 10
Views: 1,140
Posted By mido1951
yes, I use my raw Reads for mapping to the...

yes, I use my raw Reads for mapping to the reference.
and i use the default parameters for BBmap.
in this example: the global error rate is 40.9024% or 14.5421%(per bases)?
and for Sub, Del, Ins?...
Forum: Bioinformatics 01-22-2016, 03:18 PM
Replies: 10
Views: 1,140
Posted By mido1951
i used BBmap for mapping. it is a good tool? ...

i used BBmap for mapping. it is a good tool?
this is my result:


------------------ Results ------------------

Genome: 1
Key Length: 13
Max Indel: ...
Showing results 1 to 25 of 123

 


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