SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 32
Search took 0.01 seconds.
Search: Posts Made By: figo1019
Forum: RNA Sequencing 06-06-2014, 05:24 AM
Replies: 1
Views: 1,801
Posted By figo1019
Calling SNP in RNA seq

Hi All

I have assembled two mammalian transcriptome which doesn't have reference genome. I have assembled it using Trinity and now I have used varscan to call the SNP by mapping the reads to the...
Forum: RNA Sequencing 04-07-2014, 09:58 AM
Replies: 2
Views: 3,171
Posted By figo1019
Adapter trimming

Hi

I have got the adapter sequences from company as for Illumina RNA seq data:...
Forum: Illumina/Solexa 04-05-2014, 02:39 AM
Replies: 1
Views: 1,336
Posted By figo1019
Index sequences

Hi All

I recently got RNA seq data sequenced on Illumina, which is of single sample run on single lane. When I checked the RNA seq reads which are 94 bp in length, in RNA seq header I find that it...
Forum: Illumina/Solexa 04-09-2013, 05:42 AM
Replies: 9
Views: 4,225
Posted By figo1019
Hi Hsueh-Ting Chu I tried to run the...

Hi Hsueh-Ting Chu

I tried to run the EBARDenovo with the example files provided in the sample. It works fine, but when I try to run my sequences I am getting the error. I am copying the log file...
Forum: 454 Pyrosequencing 02-21-2013, 05:36 AM
Replies: 1
Views: 1,844
Posted By figo1019
Newbler Scafolding

Hi All

I tried running the newbler 2.6. But when i use the flag -scaffold I don't get any of the three scaffold file. Can some body tell me is it possible to make scaffolds using the single end...
Forum: Illumina/Solexa 01-25-2013, 07:39 AM
Replies: 1
Views: 1,019
Posted By figo1019
Tophat mapping Results

Hi All

I used tophat to map my 100 million base paired illumina reads after trimming with average length of 86 bp. In the bam output file generated by tophat I only find around 55 million read...
Forum: RNA Sequencing 01-11-2013, 03:44 AM
Replies: 38
Views: 18,134
Posted By figo1019
Hi Kenietz I have send you a personal...

Hi Kenietz

I have send you a personal message

Regard
Forum: Bioinformatics 01-08-2013, 01:51 AM
Replies: 0
Views: 1,214
Posted By figo1019
Orthomcl for more then 2 species

Hi All

I have run the orthomcl for 4 species and having the orthologous pairs file and group file. I am confused that from these files how I can take out the 4 species orthologous sequences ids as...
Forum: Bioinformatics 01-07-2013, 09:31 AM
Replies: 9
Views: 2,712
Posted By figo1019
Hi newbietonextgen I am also facing the...

Hi newbietonextgen

I am also facing the similar problem.Have you sorted it out?

Regards
Forum: RNA Sequencing 01-07-2013, 07:55 AM
Replies: 8
Views: 3,847
Posted By figo1019
Hi edge Have you figured it out that how to...

Hi edge

Have you figured it out that how to get the SNP result from RNA seq data. I also want to know.

regards
Forum: RNA Sequencing 12-06-2012, 01:16 AM
Replies: 37
Views: 19,403
Posted By figo1019
setting up the -r parameter in tophat

Hi Glados

Reading the thread and your comments. I have a query about setting up the parameter in -r. I also tried to get the information of insert size from the sequencing lab and they said me it...
Forum: Illumina/Solexa 11-18-2012, 12:02 PM
Replies: 2
Views: 5,760
Posted By figo1019
PolyA removal from RNA seq Illumina reads

Hi All,

I have paired end RNA seq Illumina reads. Do i need to remove the PolyA from the reads ( is it required) in the preprocessing step of Reads. What are the software to do it? .I am little...
Forum: RNA Sequencing 10-27-2012, 10:00 AM
Replies: 3
Views: 2,102
Posted By figo1019
Hi , I am trying with the BLASTX with the Amino...

Hi , I am trying with the BLASTX with the Amino acids of the reference genome. Another way also can be try BLAT with the Transcriptome and take out the best hits and make the alignment. Some one...
Forum: Bioinformatics 10-09-2012, 12:47 AM
Replies: 3
Views: 1,626
Posted By figo1019
Hello Meher I am also getting a similar...

Hello Meher

I am also getting a similar problem using the mpile up, have you sorted out this problem?

Regards
Forum: Bioinformatics 10-09-2012, 12:38 AM
Replies: 2
Views: 1,680
Posted By figo1019
Dear Torst Thank you for your reply. 1....

Dear Torst

Thank you for your reply.

1. I am using the samtools 0.1.18 version.
2. I tried what you suggested and I didn't get the error this time but it again stops at the same point and I...
Forum: Illumina/Solexa 10-09-2012, 12:34 AM
Replies: 3
Views: 1,844
Posted By figo1019
Thank you for your reply. 1.Please let me know...

Thank you for your reply.
1.Please let me know why it can happen as I can generate 10 chromosomes in the consensus file and then it gives the error but i can see all the chromosomes in the bam...
Forum: Bioinformatics 10-05-2012, 10:51 AM
Replies: 8
Views: 4,929
Posted By figo1019
Thank you for your reply I ran the picard...

Thank you for your reply

I ran the picard tool to validate I get an error
ERROR: Read groups is empty

Rest things are OK.

Does it make a huge difference ?

regards
Forum: Bioinformatics 10-05-2012, 07:04 AM
Replies: 8
Views: 6,348
Posted By figo1019
I am also fed up of similar error [afs]...

I am also fed up of similar error
[afs] 0:99774.498 1:110.438 2:115.064
[bcf_sync] incorrect number of fields (4 != 5) at 15:16294867

Have you found the reason for it . If you can share that...
Forum: Bioinformatics 10-05-2012, 06:07 AM
Replies: 2
Views: 1,680
Posted By figo1019
Samtools consensus sequence error

Dear All

I am again posting this question to the Bioinformatics forum as I didn't get the answer from the Illumina forum.

I am trying to make consensus sequences using command
samtools...
Forum: Illumina/Solexa 10-05-2012, 01:12 AM
Replies: 3
Views: 1,844
Posted By figo1019
Samtools consensus sequence error

Dear All

I am trying to make consensus sequences using command
samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq.
But i am getting this error:

[bcf_sync]...
Forum: Bioinformatics 10-05-2012, 12:05 AM
Replies: 8
Views: 4,929
Posted By figo1019
Hi Mark.hz Have you sorted out this problem...

Hi Mark.hz

Have you sorted out this problem as I am also facing the similar error while running the bcf file [bcf_sync] incorrect number of fields (4 != 5) at 15:16294867.

Regards
Forum: Bioinformatics 09-27-2012, 09:16 AM
Replies: 6
Views: 3,727
Posted By figo1019
Hi seqfan05 Have you sorted out the problem...

Hi seqfan05

Have you sorted out the problem as I am facing the same problem and there is not much help reading posts.

regards
Forum: RNA Sequencing 09-27-2012, 09:02 AM
Replies: 38
Views: 18,134
Posted By figo1019
Hi Kenietz Can you upload your script for...

Hi Kenietz

Can you upload your script for doing the things it will be great as I am also trying the same thing to do

Regards
Forum: Illumina/Solexa 09-06-2012, 02:41 AM
Replies: 0
Views: 1,128
Posted By figo1019
Tophat -r parameter setting

Hi All

I need to set the -r paramter in Tophat run, reading the posts on this made me confused. I have an insert size of 180 and the paired end reads of read length of size 100. So what would be...
Forum: Bioinformatics 07-25-2012, 06:56 AM
Replies: 9
Views: 1,951
Posted By figo1019
tophat running error

hi All

I have installed the tophat with bowtie and samtools in the path but I am getting the error when I try to run the example file.
[2012-07-25 17:31:11] Beginning TopHat run (v2.0.4)...
Showing results 1 to 25 of 32

 


All times are GMT -8. The time now is 05:33 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO