SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 68
Search took 0.02 seconds.
Search: Posts Made By: paa6
Forum: Bioinformatics 08-21-2015, 12:20 AM
Replies: 0
Views: 444
Posted By paa6
prophage in bacteria, what should I do next?

Hello friends, I am working on a bacterial genome and I have found 1 complete phage intact with the bacterial genome hence it's a prophage. I have found some traces of tail and head of other prophage...
Forum: Bioinformatics 04-01-2015, 08:55 PM
Replies: 2
Views: 1,427
Posted By paa6
how to create annotation table

Currently, I am dealing with bacterial genome. I have tried to predict cds by glimmer, fgenesb and classic rast. Until now I was trying to create annotation table by comparing all cds by already...
Forum: Bioinformatics 04-01-2015, 08:51 PM
Replies: 1
Views: 1,213
Posted By paa6
in my opinion NNNNNNN shows gaps. may be u need...

in my opinion NNNNNNN shows gaps. may be u need to check quality of ur reads before going for assembly. try FastQC.
Forum: Bioinformatics 04-10-2014, 10:14 PM
Replies: 14
Views: 1,669
Posted By paa6
I have used fastx_toolkit for trimming adapters....

I have used fastx_toolkit for trimming adapters. http://hannonlab.cshl.edu/fastx_toolkit/
it's actually good and for trimming adapters u should use FASTA/Q Clipper.
Forum: General 04-10-2014, 10:11 PM
Replies: 17
Views: 5,301
Posted By paa6
[QUOTE=genetics_jo;137017]Unfortunately, I...

[QUOTE=genetics_jo;137017]Unfortunately, I submitted the job as an SGE_Batch script and cannot see the output to determine if it's stuck. In the past when things have gone awry, velvet has simply...
Forum: Bioinformatics 04-08-2014, 06:15 PM
Replies: 9
Views: 4,268
Posted By paa6
I did try velvet before but now I am using...

I did try velvet before but now I am using velvetoptimiser. It's all that I am unable to understand results properly because there is no clear explanation for that..so can u give me some links for...
Forum: Bioinformatics 04-08-2014, 01:00 AM
Replies: 9
Views: 4,268
Posted By paa6
I have also used velvetoptimiser recently but...

I have also used velvetoptimiser recently but unable to understand result...can u please give me some hints how to start....I would really appreciate ur time...
Forum: Bioinformatics 04-08-2014, 12:57 AM
Replies: 1
Views: 794
Posted By paa6
yes this is a very good software for above all...

yes this is a very good software for above all tasks...I have used this software for my assembly...it's a pretty good one
Forum: Bioinformatics 04-08-2014, 12:55 AM
Replies: 1
Views: 656
Posted By paa6
velvetopimiser result

I have tried velvetoptimiser...and now I got my results but I am not able to understand them at all. in my log file there are so many cov values. I have given -s (lower end of hash value) = 19 and -e...
Forum: Bioinformatics 03-26-2014, 10:50 PM
Replies: 15
Views: 4,075
Posted By paa6
am sorry but again I am getting error ...

am sorry but again I am getting error
singhparul@ubuntu:~/trim_ends$ java -ea -Xmx1g -cp /path/to/current/ jgi.BBDukF in=Illumina_raw_reads.fastq out=clean.fastq ktrim=r k=13 literal=AGATCGGAAGAGC...
Forum: Bioinformatics 03-26-2014, 09:17 PM
Replies: 15
Views: 4,075
Posted By paa6
I HAVE TRIED THIS WAY TOO..... but still getting...

I HAVE TRIED THIS WAY TOO..... but still getting error
singhparul@ubuntu:~/Desktop$ chmod +x bbduk.sh
singhparul@ubuntu:~/Desktop$ sh ./bbduk.sh
./bbduk.sh: 84: ./bbduk.sh: Bad substitution...
Forum: Bioinformatics 03-26-2014, 08:41 PM
Replies: 15
Views: 4,075
Posted By paa6
[QUOTE=Brian Bushnell;136213]Just unzip and untar...

[QUOTE=Brian Bushnell;136213]Just unzip and untar the file you download, then you can run the shellscripts.[/QUOTE
I did unzip and untar after that I gave code like u said but I am getting this...
Forum: Bioinformatics 03-26-2014, 05:15 AM
Replies: 23
Views: 4,971
Posted By paa6
http://www.biostars.org/p/911/ may be this will...

http://www.biostars.org/p/911/
may be this will help
Forum: Bioinformatics 03-26-2014, 05:14 AM
Replies: 23
Views: 4,971
Posted By paa6
hmm I guess that depends on the version of...

hmm I guess that depends on the version of illumina reads..I haven't seen five numerical...so I got confuse!!!
but it means this is fastq format that's for sure..
Forum: Bioinformatics 03-26-2014, 05:06 AM
Replies: 15
Views: 4,075
Posted By paa6
Actually I have tried brian idea but the problem...

Actually I have tried brian idea but the problem is nothing is mentioned in site how to install it neither he mentioned it so I am thinking to give try to trimmomatic...
Forum: Bioinformatics 03-26-2014, 04:58 AM
Replies: 23
Views: 4,971
Posted By paa6
may possible that file is corrupted..... I...

may possible that file is corrupted.....

I have again gone through ur file and I have found that ur file has every element for being illumina fastq format except there is something is unusual...
Forum: Bioinformatics 03-26-2014, 02:29 AM
Replies: 23
Views: 4,971
Posted By paa6
ahhh no need to be formal by the way...and I am...

ahhh no need to be formal by the way...and I am not sir..I am mam...I have analysed ur file and this is fastq file...and use fastqc for analysis of ur sequence before doing anything further.......
Forum: Bioinformatics 03-25-2014, 10:43 PM
Replies: 23
Views: 4,971
Posted By paa6
HMM I will suggest u not to convert the file...

HMM I will suggest u not to convert the file format because it's really useless from my experience in this case. I had the same problem and infact what i faced that after converting it into fastq i...
Forum: Bioinformatics 03-25-2014, 08:58 PM
Replies: 15
Views: 4,075
Posted By paa6
I know what u meant by trueseq. adapters and I...

I know what u meant by trueseq. adapters and I know they r pretty long. Actually in my fastqc report I got error in Sequence duplication level. And I got warning in overrepresented sequences....
I...
Forum: Bioinformatics 03-25-2014, 06:49 PM
Replies: 15
Views: 4,075
Posted By paa6
thanks for quick reply , I will try this one.....

thanks for quick reply , I will try this one.. but I am using single end Illumina reads....and my adapters are default ones from trueseq. which means I have 13 bases AGATCGGAAGAGC.
please tell me...
Forum: Bioinformatics 03-25-2014, 06:16 PM
Replies: 26
Views: 6,509
Posted By paa6
how to install cutadapt

It only works in root...I did write this coding apt-get install python-dev
and I got this
Reading package lists... Done
Building dependency tree
Reading state information... Done...
Forum: Bioinformatics 03-25-2014, 05:25 PM
Replies: 15
Views: 4,075
Posted By paa6
how to install cutadapt in ubuntu 12.04

I have tried everything.......from installing python2.7 to python 3.3 and then installing cython as well.....but I get error everytime while installing cutadapt...I am working on root as well..
...
Forum: Illumina/Solexa 03-10-2014, 01:31 AM
Replies: 4
Views: 2,504
Posted By paa6
ohh ok thanks!!!

ohh ok thanks!!!
Forum: Illumina/Solexa 03-09-2014, 10:40 PM
Replies: 4
Views: 2,504
Posted By paa6
THanks for the quick reply!! I have typed $ grep...

THanks for the quick reply!! I have typed $ grep -c 'GATCGGAAGAGC' reads.fastq
and I got 28875..what is this mean??
also I am doing SE assembly while skewer is for PE...
Forum: Illumina/Solexa 03-09-2014, 09:07 PM
Replies: 4
Views: 2,504
Posted By paa6
how ro see adapter contamination in Illumina reads

I have illumina read file..which is bacterial DNA sequence...I have used geneious software to assembly it, while assembly I have found that there was vector contamination and it was removed by...
Showing results 1 to 25 of 68

 


All times are GMT -8. The time now is 06:26 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO