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Search: Posts Made By: nareshvasani
Forum: Bioinformatics 12-11-2014, 10:35 AM
Replies: 17
Views: 5,225
Posted By nareshvasani
Thanks Brian and westerman for your input and...

Thanks Brian and westerman for your input and suggestion
Forum: Bioinformatics 12-11-2014, 08:52 AM
Replies: 17
Views: 5,225
Posted By nareshvasani
ohh okay. I don't have much expertise in...

ohh okay.

I don't have much expertise in system administraion.
Actually I installed new bowtie2 version but I was not able to excetue it. Whenever I type bowtie2, only older version will work not...
Forum: Bioinformatics 12-11-2014, 08:08 AM
Replies: 17
Views: 5,225
Posted By nareshvasani
Hey Westerman, I installed new version but I...

Hey Westerman,

I installed new version but I was not succesful to use it, so i decided to stick with older version (Bowtie 2 version 2.0.0-beta5)

One interesting thing happen, when I terminated...
Forum: Bioinformatics 12-11-2014, 07:40 AM
Replies: 17
Views: 5,225
Posted By nareshvasani
Hi Westerman, Thanks for your prompt reply....

Hi Westerman,

Thanks for your prompt reply. I used -M option for below reason.

-M <int> look for up to <int>+1 alns; report best, with MAPQ (5 for --end-to-end, 2...
Forum: Bioinformatics 12-11-2014, 07:10 AM
Replies: 17
Views: 5,225
Posted By nareshvasani
Hi Westerman, I am using bowtie2 for rRNA...

Hi Westerman,

I am using bowtie2 for rRNA removal:

Step1: Create Index

# bowtie2-build rRNA.fasta rRNA.index

Step 2: Align to rRNA index inorder to get rRNA free fastq file.
Input...
Forum: Bioinformatics 12-11-2014, 06:04 AM
Replies: 7
Views: 2,114
Posted By nareshvasani
Hi jpnm, Thanks for your input, I am trying...

Hi jpnm,

Thanks for your input, I am trying you suggestion. Will keep you posted.


Naresh
Forum: Bioinformatics 12-10-2014, 11:53 AM
Replies: 7
Views: 2,114
Posted By nareshvasani
Hi fellow, I am trying to find rRNA gene...

Hi fellow,

I am trying to find rRNA gene from my input file:

Step1: Create Index

#bowtie2-build rRNA.fasta rRNA.index

Step 2: Align to rRNA index inorder to get rRNA free fastq file.
Forum: Bioinformatics 09-09-2014, 06:06 AM
Replies: 6
Views: 4,335
Posted By nareshvasani
Smile Thanks Brian for your prompt reply. Naresh

Thanks Brian for your prompt reply.

Naresh
Forum: Bioinformatics 09-09-2014, 06:06 AM
Replies: 6
Views: 4,335
Posted By nareshvasani
Smile Hi Gringer, Thanks for your quick response. ...

Hi Gringer,

Thanks for your quick response.
What I did was, used existing assembly as reference and whichever sequence's or read's were not matched to reference, I extracted those read and...
Forum: Bioinformatics 09-08-2014, 08:35 AM
Replies: 6
Views: 4,335
Posted By nareshvasani
Smile Merge 2 de novo assembly generated using Trinity!

Hi Criggs!

I am also trying to merge assembly which were generated using trinity.
After merging assembly, I found that there were 2 same transcipt id in merged assembly.
Could you please tell me...
Forum: De novo discovery 05-21-2014, 06:08 AM
Replies: 26
Views: 12,538
Posted By nareshvasani
Smile Hi Sabbir, This cmd I used for my data....

Hi Sabbir,


This cmd I used for my data. You do not have to follow same steps but you have to use this cmd as your reference as per your data need [as said bu Genomax]

I think you have not...
Forum: De novo discovery 05-20-2014, 12:46 PM
Replies: 26
Views: 12,538
Posted By nareshvasani
Smile Hi Sabbir, Below are the following steps I...

Hi Sabbir,

Below are the following steps I used for trimming:

The following command keep reads which has quality score above 20 in at least 50% of bases.
> fastq_quality_filter -Q33 -q20 -p 50...
Forum: De novo discovery 05-19-2014, 06:02 AM
Replies: 26
Views: 12,538
Posted By nareshvasani
Smile Hi Sabbir, How did you confirm that assembly...

Hi Sabbir,

How did you confirm that assembly from MIRA4, Trinity and velvet assembler were not good enough?
I had very big input file (fastq) which was not very well handled by all assembler. So,...
Forum: Bioinformatics 02-27-2014, 05:47 AM
Replies: 45
Views: 13,905
Posted By nareshvasani
Smile Install the library either by using Ubuntu...

Install the library either by using Ubuntu software center/method below:

Code:
$sudo apt-get install libgtextutils0

Best,
Naresh:)
Forum: Ion Torrent 01-28-2014, 12:26 PM
Replies: 7
Views: 3,619
Posted By nareshvasani
Smile Hi sklages, I contacted them, they just...

Hi sklages,

I contacted them, they just told me get new computer resources with more GB on it.

Thanks,
Naresh:)
Forum: Ion Torrent 01-28-2014, 12:25 PM
Replies: 7
Views: 3,619
Posted By nareshvasani
Smile SPAdes

Hi akorobeynikov,

Thanks for your reply. I am doing transcriptome analysis and SPAdes is useful for only genome analysis.
Am i right?

Best,
Naresh
Forum: De novo discovery 12-11-2013, 07:49 AM
Replies: 2
Views: 6,407
Posted By nareshvasani
Post Nice explaination Pseudonym... :)

Nice explaination Pseudonym...
:)
Forum: Ion Torrent 11-06-2013, 07:36 AM
Replies: 7
Views: 3,619
Posted By nareshvasani
Hi Users, bump....

Hi Users,

bump....
Forum: Ion Torrent 10-30-2013, 12:46 PM
Replies: 7
Views: 3,619
Posted By nareshvasani
Mira4 Assembler using all memory for denovo, est assembly

Hi Users,

My PC has 48 GB of RAM and 8 CPU. I am trying to create denovo assembly using Mira 4 Assembler. Input file has only 2 fastq files with only 30 million reads with sequence length 50-350...
Forum: RNA Sequencing 09-25-2013, 07:59 AM
Replies: 23
Views: 68,340
Posted By nareshvasani
Smile I did the same way. Thanks for feedback.

I did the same way.

Thanks for feedback.
Forum: RNA Sequencing 09-25-2013, 07:59 AM
Replies: 23
Views: 68,340
Posted By nareshvasani
Thanka a bunch. :)

Thanka a bunch.
:)
Forum: Ion Torrent 08-27-2013, 07:39 AM
Replies: 1
Views: 5,432
Posted By nareshvasani
Post de novo Transcriptome analysis to get differential expression data

Hello All User,

I need your help with downstream analysis. I have fastq file containing sinlge end read from ion proton instrument. I have generated de novo assembly using Trinity.
From there on...
Forum: De novo discovery 08-23-2013, 09:23 AM
Replies: 26
Views: 12,538
Posted By nareshvasani
Post Hi

Hi everyone,

I run below cmd for alignment.
bin/util/alignReads.pl --seqType fq --single CombineIonXpressRNA_010_NareshPool_Chip1_2_WT2_fastxtrimmer_from_quality_trimmer.fastq --target...
Forum: De novo discovery 08-23-2013, 08:35 AM
Replies: 26
Views: 12,538
Posted By nareshvasani
Post Hi Genomax,

Thanks for feedback.

I don't have paired end data.
I was confused about output of alignReads.pl script. i.e. how to confirm percentage of alignment. That's why asked about pairing. Sorry about...
Forum: De novo discovery 08-23-2013, 07:59 AM
Replies: 26
Views: 12,538
Posted By nareshvasani
Post Thanks, If I use bowtie, does it make any...

Thanks,

If I use bowtie, does it make any difference in alignment.
When I am running cmd with bowtie, while processing it shows below message:
CMD: bowtie -k 20 -S --sam-nohead -q target...
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