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Search: Posts Made By: Charitra
Forum: Bioinformatics 07-30-2013, 06:16 PM
Replies: 9
Views: 8,145
Posted By Charitra
Question Hi The the scores are available there but...

Hi
The the scores are available there but fusion-post filters the total fusions.
I have a question about tophat insert size commands, say insertsize 100~380(main 150); how can we modify in tophat...
Forum: Bioinformatics 07-09-2013, 04:07 PM
Replies: 6
Views: 2,972
Posted By Charitra
Yes, I am using cummeRbund.

Yes, I am using cummeRbund.
Forum: Bioinformatics 07-09-2013, 06:04 AM
Replies: 6
Views: 2,972
Posted By Charitra
Please tell me how you have managed to do. I need...

Please tell me how you have managed to do. I need to make heatmap with -1 0 +1 range (not the log 10 RPKM value).
Can you reply please.
Thank you
:confused:
Forum: Bioinformatics 07-09-2013, 12:35 AM
Replies: 6
Views: 2,972
Posted By Charitra
did you get the answer?:confused: :confused:

did you get the answer?:confused:

:confused:
Forum: Bioinformatics 07-08-2013, 06:39 PM
Replies: 42
Views: 20,813
Posted By Charitra
Smile Dear nls Thank you so much for your expert...

Dear nls
Thank you so much for your expert comments :) . I got the point and thank you again for your help:).
I like to write details on your comments no. 3. and 4. :
3. My first two sample (1....
Forum: Bioinformatics 07-04-2013, 11:44 PM
Replies: 2
Views: 2,141
Posted By Charitra
I am also trying to find TSS in my cuffdiff data...

I am also trying to find TSS in my cuffdiff data :confused:
Forum: RNA Sequencing 07-04-2013, 11:42 PM
Replies: 1
Views: 1,686
Posted By Charitra
Looking for the same :confused:

Looking for the same :confused:
Forum: Bioinformatics 07-04-2013, 11:39 PM
Replies: 5
Views: 5,629
Posted By Charitra
Is anybody out there to answer this question ? I...

Is anybody out there to answer this question ? I looking for an answer too.:confused:
Forum: RNA Sequencing 07-04-2013, 11:35 PM
Replies: 1
Views: 2,866
Posted By Charitra
I am in the same boat. did anybody get answer ? ...

I am in the same boat. did anybody get answer ?
:confused:
Forum: Bioinformatics 07-04-2013, 09:48 PM
Replies: 42
Views: 20,813
Posted By Charitra
Thank you so much for your expert comments. I...

Thank you so much for your expert comments.
I have some confusions/questions but searching the answers in previous posts. I will drop my questions here, if I can not find the answers.

However,...
Forum: Bioinformatics 07-04-2013, 01:02 AM
Replies: 42
Views: 20,813
Posted By Charitra
So, does it mean that all reference files must be...

So, does it mean that all reference files must be from same origin (ensembl or UCSC) ?
Is it okay to ignore this warning (Warning: No conditions are replicated, switching to 'blind' dispersion...
Forum: RNA Sequencing 06-23-2013, 11:03 PM
Replies: 25
Views: 7,191
Posted By Charitra
Dear GenoMax, I got cuffdiff results and , i...

Dear GenoMax,
I got cuffdiff results and , i think, gene name or somthing went wrong which was giving warnings because i can not fined my gene in cummeRbund but gene is there in database when i...
Forum: Bioinformatics 06-23-2013, 10:58 PM
Replies: 15
Views: 16,412
Posted By Charitra
Dear shabhonam I got another problem with...

Dear shabhonam
I got another problem with cuffdiff or cummeRbund.
in R cummeRbund, it can not find gene but gene is there in my cuffdiff output when I checked manually ... is this errog in cuffdiff...
Forum: Bioinformatics 06-18-2013, 06:44 PM
Replies: 33
Views: 36,809
Posted By Charitra
Question Hi Starr I am facing problem with...

Hi Starr

I am facing problem with cummeRbund, I searched manually RBBP8 in cuffdiff results and is there but cummeRbund can not find it when I try mygene<-getGene(cuff_data,'RBBP8"). Other genes...
Forum: RNA Sequencing 06-18-2013, 03:23 AM
Replies: 61
Views: 35,874
Posted By Charitra
Dear All I got problem with cummeRbund.... my...

Dear All
I got problem with cummeRbund.... my RNA-seq data has fusion gene HLA-DQB1. When I conducted diff analysis (cufflinks), cummeRbund can not show this gene. I tried HLA-DQB1, HLADQB1, HLADQB,...
Forum: Bioinformatics 06-05-2013, 12:05 AM
Replies: 40
Views: 18,586
Posted By Charitra
For the Paired end, I am not able to say...

For the Paired end, I am not able to say anything.
prefer to use -o tophat_PRO

nothing more to say/
Forum: Bioinformatics 06-04-2013, 08:38 PM
Replies: 40
Views: 18,586
Posted By Charitra
Hi there, Can you compare the two commands: ...

Hi there,
Can you compare the two commands:

tophat -o /path/to/sample/tophat_PRO -p 8 --fusion-search --keep-fasta-order --bowtie1 --no-coverage-search -r 0 --mate-std-dev 80 --max-intron-length...
Forum: Bioinformatics 06-04-2013, 04:08 PM
Replies: 40
Views: 18,586
Posted By Charitra
Please read my last post. check the output...

Please read my last post. check the output directory name, if it is different then you will get 0 fusion. and.. try chimerascan is the best for fusion.
Please reply if you get error again.
Charitra
Forum: Bioinformatics 04-26-2013, 05:52 PM
Replies: 23
Views: 43,154
Posted By Charitra
Unhappy Is there a single command to sort .bam output of...

Is there a single command to sort .bam output of tophat "samtools sort aln.bam aln.sorted"

or there is a bunch of commands which I have to use... ?

any idea please ?
Forum: Bioinformatics 04-24-2013, 06:32 PM
Replies: 16
Views: 5,369
Posted By Charitra
I got confusions again and posted here...

I got confusions again and posted here http://seqanswers.com/forums/showthread.php?p=102818#post102818

is there anything to add large bundle ?

I got he answer for my questions... cufflinks...
Forum: Bioinformatics 04-24-2013, 06:30 PM
Replies: 14
Views: 30,209
Posted By Charitra
Unhappy I got he same error [bam_header_read] EOF marker...

I got he same error [bam_header_read] EOF marker is absent.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File ./merged_asm/tmp/mergeSam_filepsu0Hv doesn't appear to be a...
Forum: Bioinformatics 04-24-2013, 05:02 AM
Replies: 16
Views: 5,369
Posted By Charitra
Yes Dear Helical and GenoMax I used -G for...

Yes Dear Helical and GenoMax

I used -G for aligning using tophat and then -g in cuffmerge.
Forum: Bioinformatics 04-24-2013, 04:45 AM
Replies: 16
Views: 5,369
Posted By Charitra
Red face I got one solution here...

I got one solution here http://seqanswers.com/forums/showthread.php?p=102646#post102646 please see my complete log details in attachment...

these seems to be lincRNA or pseudo... and excluded from...
Forum: RNA Sequencing 04-23-2013, 04:34 PM
Replies: 25
Views: 7,191
Posted By Charitra
Dear GenoMax I got one doubt, if there are...

Dear GenoMax

I got one doubt, if there are lincRNA's and I just ignore them, then I am trying to differentiate the expression level in my samples. Sometimes, these are needed for differentiation...
Forum: RNA Sequencing 04-23-2013, 05:55 AM
Replies: 25
Views: 7,191
Posted By Charitra
Results are there... I have not yet analysed...

Results are there... I have not yet analysed properly... I just got the output from R but didnt read the results from R... results are not empty... there are genes but there is not significant...
Showing results 1 to 25 of 57

 


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