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Forum: Bioinformatics 09-28-2018, 11:50 AM
Replies: 0
Views: 731
Posted By Medhat
TLEN field explained

If the TLEN value is Zero; it means information is unavailable, (I think this means that the alignment does not make sense from biological point if view right?)?
How can I get more info about the...
Forum: General 11-06-2017, 01:16 AM
Replies: 1
Views: 1,317
Posted By Medhat
PBSuite spots ambiguous insertion output value

Hi,

Originally I post this question in another place but I could not find an answer.

I am using PBSuite version 15.8.24

`Honey.py spots` was used to identify structure variations.

here is...
Forum: Bioinformatics 07-19-2017, 06:07 AM
Replies: 7
Views: 5,517
Posted By Medhat
[QUOTE=Brian Bushnell;134401]This is not correct...

[QUOTE=Brian Bushnell;134401]This is not correct - if there are two equal-scoring locations, bwa gives both a mapping score of 3 (equivalent to 50% probability), and so forth.

what about duplicate...
Forum: Bioinformatics 07-19-2017, 05:59 AM
Replies: 7
Views: 5,517
Posted By Medhat
what about duplicate how BWA deals with duplicate...

what about duplicate how BWA deals with duplicate , and Is it possible to give me the source of this info.
Forum: Introductions 07-19-2016, 09:28 AM
Replies: 6
Views: 2,405
Posted By Medhat
this one VAAST...

this one VAAST (http://www.yandell-lab.org/software/vaast.html)
Forum: Introductions 07-19-2016, 03:30 AM
Replies: 6
Views: 2,405
Posted By Medhat
http://www.yandell-lab.org/software/vaast.html ...

http://www.yandell-lab.org/software/vaast.html

have such tool
Forum: Pacific Biosciences 05-10-2016, 01:21 AM
Replies: 4
Views: 1,526
Posted By Medhat
First it uses short reads, If there is no short...

First it uses short reads, If there is no short reads it uses long reads, now as rhall mentioned it uses long reads only in a new software called canu
Forum: Pacific Biosciences 04-20-2016, 05:40 AM
Replies: 3
Views: 1,996
Posted By Medhat
Unfortunately the raw read coverage is low ~1x ,...

Unfortunately the raw read coverage is low ~1x , so I can not go for canu.

To run celera assembler

runCA -d directory -p prefix myPacBio.frg

How to create myPacBio.frg from corrected...
Forum: Pacific Biosciences 04-15-2016, 05:11 AM
Replies: 3
Views: 1,996
Posted By Medhat
Question Genome assembly Using Celera Assembler with corrected data from LoRDEC

Hi,
I corrected PacBio reads Using LoRDEC tool , now I have a corrected fasta file.
My question,
Can I use Celera Assembler with the corrected reads from LoRDEC to do assembly?
Forum: Bioinformatics 03-09-2016, 08:30 AM
Replies: 3
Views: 1,021
Posted By Medhat
No, but I do have the package now, and I do not...

No, but I do have the package now, and I do not remember exactly how I overcome it.
Forum: Bioinformatics 01-12-2016, 01:19 AM
Replies: 0
Views: 1,480
Posted By Medhat
Exclamation Mafft mismatch value

Hi,

I tried to find both in
http://mafft.cbrc.jp/alignment/software/manual/manual.html
and
http://mafft.cbrc.jp/alignment/software/algorithms/algorithms.html

to find the nucleotide...
Forum: Pacific Biosciences 08-18-2015, 05:19 AM
Replies: 0
Views: 1,448
Posted By Medhat
Exclamation what is third column in the log file output for pacBioToCa

I used pacBioToCa to correct some long reads LR using illumina short reads SR

from the log file there is this info:


INPUT_NAME OUTPUT_NAME SUBREAD START END LENGTH
S1_1217...
Forum: Pacific Biosciences 07-30-2015, 02:13 AM
Replies: 0
Views: 1,020
Posted By Medhat
Exclamation can I use PBcR only for correction with out assembly?

can I use the PBcR from http://wgs-assembler.sourceforge.net/wiki/index.php/PBcR

only to correct pacbio reads with illumina with out assembling the genome?
Forum: Bioinformatics 06-23-2015, 06:12 AM
Replies: 3
Views: 1,021
Posted By Medhat
Exclamation error in compiling Whole-Genome Shotgun Assembler

following this link
https://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/wgs-8.3/

I am trying to install the package
But when use this command

cd src && make && cd ..

I...
Forum: Bioinformatics 06-10-2015, 02:38 AM
Replies: 0
Views: 1,767
Posted By Medhat
Exclamation "buffer overflow detected" when using SInC simulator

I am using SInC simulator , command is;

./SInC_simulate -S 0.002 -I 0.0001 -p 0 /data/genome.fa > ./illumina_read

It gives ;

*** buffer overflow detected ***: ./SInC_simulate terminated...
Forum: Bioinformatics 05-22-2015, 12:08 AM
Replies: 1
Views: 929
Posted By Medhat
Blast2Go a simple yet powerful tool to make...

Blast2Go a simple yet powerful tool to make Blast,Mapping,Annotation
https://www.blast2go.com/

Or

using pfam to search for protein with hmmer
ftp://ftp.sanger.ac.uk/pub/databases/Pfam/Tools/
Forum: Bioinformatics 02-11-2015, 01:13 AM
Replies: 2
Views: 1,306
Posted By Medhat
bam2pindel Error

Hi,

I am trying to use bam2pindel using this command:
perl bam2pindel.pl -i ./sorted_ByName.bam -o ./pindel -s s79757 -pi 400

It gives me this error:

Forked pipe to run:...
Forum: Bioinformatics 09-29-2014, 01:35 AM
Replies: 62
Views: 28,584
Posted By Medhat
Hi, First I used Then I used...

Hi,

First I used



Then I used your software as:
Forum: Pacific Biosciences 09-17-2014, 01:46 AM
Replies: 29
Views: 7,657
Posted By Medhat
so to make sure that I understand correctly first...

so to make sure that I understand correctly first I will copy the files from this directory;


Note:
I have in


four jobs
016452 016451 016450 016438
Forum: Pacific Biosciences 09-16-2014, 02:32 AM
Replies: 29
Views: 7,657
Posted By Medhat
any new sugeestions?

any new sugeestions?
Forum: Pacific Biosciences 09-12-2014, 01:15 AM
Replies: 29
Views: 7,657
Posted By Medhat
Using this command every thing is ok...

Using this command



every thing is ok and this is the last line of the output

m140709_111451_42149_c100664292550000001823130112201495_s1_p0/163190/16535_18492 2 0 0 -6508 82.8514 133857058...
Forum: Pacific Biosciences 09-09-2014, 04:11 AM
Replies: 29
Views: 7,657
Posted By Medhat
medhat@medhat:/data/smrtAnalysis$ source...

medhat@medhat:/data/smrtAnalysis$ source /data/smrtAnalysis/current/etc/setup.sh

medhat@medhat:/data/smrtAnalysis$ pbalign.py "/data/smrtAnalysis/current/common/jobs/016/016452/input.fofn"...
Forum: Pacific Biosciences 09-08-2014, 12:19 PM
Replies: 29
Views: 7,657
Posted By Medhat
OK but why i need to source the setup.sh ?

OK but why i need to source the setup.sh ?
Forum: Pacific Biosciences 09-08-2014, 01:36 AM
Replies: 29
Views: 7,657
Posted By Medhat
on my PC single machine which is 12 cpu 32G...

on my PC single machine which is 12 cpu 32G memory

in this directory:
/data/smrtAnalysis/current/common/jobs/016/016452/log/P_Mapping

log is :
Forum: Pacific Biosciences 09-05-2014, 06:25 AM
Replies: 29
Views: 7,657
Posted By Medhat
yes I provided a reference of the genome and yet...

yes I provided a reference of the genome and yet it failed
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