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Forum: Bioinformatics 07-13-2016, 03:23 AM
Replies: 1
Views: 1,687
Posted By ron128
read trimming for small RNA NGS data

Hello all. This seems to be a routinely discussed question with many answers around here, however I could not use the answers provided in other questions to solve my query. I have some mi-RNA seq...
Forum: Bioinformatics 03-27-2014, 01:08 AM
Replies: 23
Views: 5,488
Posted By ron128
Talking The mystery Deepens

@ Mr Ryan: Tried what you suggested. Turns out it IS pre 1.8

Tried out solexa QA as well. Returns Casava 1.3 as the pipeline used for generating the data.

Now here is where things start to get...
Forum: Bioinformatics 03-26-2014, 10:15 AM
Replies: 23
Views: 5,488
Posted By ron128
Dear Mr Ryan, Thanks a ton for all your insights....

Dear Mr Ryan, Thanks a ton for all your insights. I am trying to run the grep command and see if it is what you are suggesting. I should have some insights by tomorrow upon greping the data, once i...
Forum: Bioinformatics 03-26-2014, 10:14 AM
Replies: 23
Views: 5,488
Posted By ron128
Thanks a ton for this! I tried solexaQA as well,...

Thanks a ton for this! I tried solexaQA as well, but guess what :D another weird error :D I have written in to solexaQA mailing list. awaiting a response.

Well I cannot know for certain whether...
Forum: Bioinformatics 03-26-2014, 04:51 AM
Replies: 23
Views: 5,488
Posted By ron128
Dear Sir/Madam, I have no clue as to what...

Dear Sir/Madam, I have no clue as to what platform was used for sequencing this data. The only thing which has been told to me is that this data is from NIH3T3 cell lines :/ the sequencing company...
Forum: Bioinformatics 03-26-2014, 03:34 AM
Replies: 23
Views: 5,488
Posted By ron128
Ahh sorry for the confusion mam! lol. anways, I...

Ahh sorry for the confusion mam! lol. anways, I wanted to use prinseq with this data, (i prefer it over fastqc because of its DUST low complexity filters as well as the plots which are more intuitive...
Forum: Bioinformatics 03-26-2014, 03:32 AM
Replies: 23
Views: 5,488
Posted By ron128
@ Mr Ryan: I might be mistaken, but i was kinda...

@ Mr Ryan: I might be mistaken, but i was kinda certain thats not a fastq format file. If you look at the fourth line, it has these weird stretches of "________" characters. what gives? I have not...
Forum: Bioinformatics 03-26-2014, 01:01 AM
Replies: 23
Views: 5,488
Posted By ron128
Thanks a lot for your insight sir! however like i...

Thanks a lot for your insight sir! however like i mentioned, the service provider has folded, and the only access to data that we have is this data here. Is there any way I can convert this data to...
Forum: Bioinformatics 03-25-2014, 10:09 PM
Replies: 23
Views: 5,488
Posted By ron128
A google search for this error reveals the...

A google search for this error reveals the following, but I am not sure how fiddling with original sequencer output files, or raw fastq files will work out.
...
Forum: Bioinformatics 03-25-2014, 10:05 PM
Replies: 23
Views: 5,488
Posted By ron128
Data format of NGS file

Hello,
I have been dealing with some strange data recently. I suspect this might be illumina's older casava (pre 1.8) output from the GAIIX. unfortunately the lab where i work at has no clue...
Forum: Bioinformatics 11-13-2013, 09:42 AM
Replies: 3
Views: 2,248
Posted By ron128
This is what I am afraid of if I blast my...

This is what I am afraid of if I blast my sequences to the NR or NT database. To circumvent this, since I am dealing with human data, I am blasting only against Human est sequences. I am hoping this...
Forum: Bioinformatics 11-13-2013, 03:45 AM
Replies: 3
Views: 2,248
Posted By ron128
Best hit alignment in offline Blast

Hello. Can anyone let me know the proper command and syntax for best hit alignment in offline blast? The blast manual lists is not very clear on this topic, and I cannot seem to find much information...
Forum: General 09-20-2013, 04:05 AM
Replies: 2
Views: 1,696
Posted By ron128
Hello, Is this still open??

Hello, Is this still open??
Forum: Bioinformatics 06-25-2013, 11:45 PM
Replies: 21
Views: 39,262
Posted By ron128
Amen! Couldnt agree more! :D IMHO though,...

Amen! Couldnt agree more! :D

IMHO though, Cufflinks-tophat is still a very viable option, inspite of the developers silence!
Forum: Bioinformatics 06-18-2013, 09:49 AM
Replies: 1
Views: 3,396
Posted By ron128
Hello, The most relevant criteria in my...

Hello, The most relevant criteria in my experience is the altered allele depth. I personally do not recalibrate my variant files, so I dont rely on the GATK quality filter score. In general, I can...
Forum: Bioinformatics 06-18-2013, 09:43 AM
Replies: 5
Views: 6,717
Posted By ron128
Mutect Analysis Criteria: Judgement Calls

Hello everybody, I am dealing with a dataset of cancer tumours sequenced on hiseq. I do not have a matched normal, and I have used Mutect to call somatic variants. I have the following doubts:

1)...
Forum: RNA Sequencing 05-20-2013, 10:31 PM
Replies: 3
Views: 1,560
Posted By ron128
Is the 2 Tb of diskspace uniformly allocated? If...

Is the 2 Tb of diskspace uniformly allocated? If there is lesser space on your home folder, this may affect the writing of files in tmp directory. At least the memory is not a constraint in this...
Forum: Bioinformatics 05-14-2013, 01:46 AM
Replies: 1
Views: 2,066
Posted By ron128
Custom reference when aligning male/ female NGS data to hg19 reference

Hello everybody. I just wanted to ask if somebody has any experience in aligning sex specific data to hg19 genome build. I recently came accross a weird problem (which when you look at it indepth...
Forum: Bioinformatics 05-14-2013, 01:40 AM
Replies: 3
Views: 1,164
Posted By ron128
Dude, Many many thanks! this is working out...

Dude, Many many thanks! this is working out absolutely fine now. Looks like i should explore more of the Unix environment tools! This has streamlined my analysis and cut down a lot of time. Thanks a...
Forum: RNA Sequencing 05-14-2013, 01:31 AM
Replies: 3
Views: 1,560
Posted By ron128
Can you check the diskspace where the files are...

Can you check the diskspace where the files are running? TOphat requires a lot of temporary space when its running and may give errors if the diskspace is full. Alternatively, have you tried running...
Forum: Bioinformatics 04-16-2013, 06:22 AM
Replies: 3
Views: 1,164
Posted By ron128
many thanks! I will try this out and post the...

many thanks! I will try this out and post the results.
Forum: Bioinformatics 04-16-2013, 02:58 AM
Replies: 3
Views: 1,164
Posted By ron128
Comparing data from two columns

Hello everybody,
I am analysing variant calls from two different pipelines. What i need to do for my downstream analysis is combine all the variant calls into a single file,...
Forum: Bioinformatics 03-30-2013, 12:33 AM
Replies: 2
Views: 2,362
Posted By ron128
Hey thanks for a quickie reply :) Like i said, I...

Hey thanks for a quickie reply :) Like i said, I am not redoing any alignments here. I have already run the tophat cufflinks pipeline on my data to assemble it into known transcripts using UCSC genes...
Forum: Bioinformatics 03-29-2013, 12:33 PM
Replies: 2
Views: 2,362
Posted By ron128
Variant Calling from paired end RNAseq data

Hello everybody, since everybody is getting on the variant calling from RNAseq bandwagon, my P.I wants to get in on the party as well. Too bad for overworked ppl like me :( So I have this huge...
Forum: Bioinformatics 01-09-2013, 11:02 PM
Replies: 3
Views: 3,268
Posted By ron128
Thanks a ton guys for a quick reply! One...

Thanks a ton guys for a quick reply!

One thing i would like to point out like i posted in my earlier thread, which everybody seems to have missed out is that this is a WGS of a MOUSE GENOME and...
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