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Forum: Bioinformatics 04-09-2015, 08:04 AM
Replies: 21
Views: 4,891
Posted By Ahaswer
Hi Joana, can you describe your failure? Have...

Hi Joana,
can you describe your failure? Have you downloaded correct release?
Forum: Bioinformatics 03-31-2015, 08:22 PM
Replies: 19
Views: 7,474
Posted By Ahaswer
Hi Brian. Yes, the reads have been...

Hi Brian. Yes, the reads have been adapter-trimmed. Moreover alignment toward long sequences (whole reference) gives good alignment rate and low while using short (miRBase) sequences.
Forum: Bioinformatics 03-31-2015, 06:12 AM
Replies: 19
Views: 7,474
Posted By Ahaswer
Thanks everybody for your replies. That satisfies...

Thanks everybody for your replies. That satisfies my curiosity, especially those papers.
Also I've checked reads alignment count for each miRNA sequence, based on miRBase annotations, which gives me...
Forum: Bioinformatics 03-31-2015, 12:38 AM
Replies: 19
Views: 7,474
Posted By Ahaswer
As you suggested I have used featureCounts to...

As you suggested I have used featureCounts to check reads location and it is more or less the same (4.6%). So it is an issue of contamination, however I will try to get some valuable data. Guess I...
Forum: Bioinformatics 03-30-2015, 01:53 PM
Replies: 19
Views: 7,474
Posted By Ahaswer
Still the same overall alignment rate. Does...

Still the same overall alignment rate. Does anyone have some suggestions about bowtie2 parameters for this task?
Forum: Bioinformatics 03-30-2015, 02:11 AM
Replies: 19
Views: 7,474
Posted By Ahaswer
Yes, I've aligned reads to the mature.fa also but...

Yes, I've aligned reads to the mature.fa also but this alignment provides me only 4.39% of overall alignment rate. As you suggested I'll try remove special characters from those files.
Forum: Bioinformatics 03-30-2015, 01:57 AM
Replies: 19
Views: 7,474
Posted By Ahaswer
I've made some research before and found opinions...

I've made some research before and found opinions that bowtie1 is not better than bowtie2 while considering miRNA data. So I'm convinced to use bowtie2 for this purpose, but still I have this problem.
Forum: Bioinformatics 03-30-2015, 12:48 AM
Replies: 19
Views: 7,474
Posted By Ahaswer
miRNA reads alignment with bowtie2

Hi everyone,

I'm working on miRNA data right now (which is very new field for me). I'm trying to filter out only those reads which belongs to miRBase. Here is my procedure.
Align all reads with...
Forum: Bioinformatics 03-23-2015, 07:23 AM
Replies: 2
Views: 921
Posted By Ahaswer
Thanks cascoamarillo, I will proceed as you...

Thanks cascoamarillo, I will proceed as you suggested. But using bowtie2 will remove also reads which are located at exons boundaries so that I will get those files in unmapped reads, am I correct?
Forum: Bioinformatics 03-23-2015, 06:27 AM
Replies: 2
Views: 921
Posted By Ahaswer
Filtering out transcriptome data

Hi,
I have RNA-Seq reads of mutant plant which has few insertions (unknown sequence) in comparison to wild reference genome. I want to filter out all reads which are the same as in reference so I...
Forum: Bioinformatics 03-18-2015, 06:29 AM
Replies: 8
Views: 3,053
Posted By Ahaswer
Hello, I'm using bowtie2, however my collegue...

Hello, I'm using bowtie2, however my collegue praises BWA. Also I have to try BBmap and compare results between those three.
Forum: Bioinformatics 02-18-2014, 11:17 PM
Replies: 0
Views: 1,096
Posted By Ahaswer
Reads amount - chloroplast genome assembly

It may be too general question, but could you tell me what should be average amount of reads (PE) used for chloroplast genome assembly (about 120-140 kbp)? I mean what are your experiences.
Forum: Introductions 02-18-2014, 11:07 PM
Replies: 0
Views: 706
Posted By Ahaswer
Smile Greetings from Poland

Hello SEQanswers users.
It's impressive what treasury of knowledge SEQanswers is. Since this day I have been passive user of this forum. Now those are my first words, hope not last :) I have been...
Showing results 1 to 13 of 13

 


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