Forum: Bioinformatics
10-27-2016, 04:51 PM
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Replies: 1
Views: 5,568
SA tag in SAM file for chimeric reads
Hi,
I am using BWA-mem for split read alignment for my single end genomic DNA-seq from Illumina. I know that BWA uses SA tag for marking chimeric reads. When I manually BLAST individual reads with...
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Forum: Illumina/Solexa
05-11-2015, 12:11 PM
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Replies: 5
Views: 1,730
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Forum: Illumina/Solexa
05-10-2015, 08:37 AM
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Replies: 5
Views: 1,730
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Forum: Illumina/Solexa
04-28-2015, 08:15 AM
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Replies: 5
Views: 1,730
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Forum: Bioinformatics
03-30-2015, 07:44 AM
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Replies: 4
Views: 4,327
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Forum: Bioinformatics
03-27-2015, 01:40 PM
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Replies: 4
Views: 4,327
Normalize small RNA data with spike-in controls?
Dear all,
I am planning to sequence small RNAs from my control and mutant cells and I was wondering what is the best way to normalize the data. My initial data shows that the small RNAs in...
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Forum: Bioinformatics
12-18-2014, 09:50 AM
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Replies: 3
Views: 975
Thanks for the prompt reply bruce01, but I...
Thanks for the prompt reply bruce01, but I thought that bedtools will report all the common overlap features between my gff and bam/bed. I only need to extract the reads which are overlapping the...
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Forum: Bioinformatics
12-18-2014, 07:20 AM
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Replies: 3
Views: 975
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Forum: Bioinformatics
07-26-2013, 09:04 AM
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Replies: 0
Views: 1,150
Normalization for RNA-IP experiment
I have some Illumina sequencing reads from two RNA-IP experiments, one utilizing the test antibody and the other with a control antibody (IgG). I did a small scale sequencing and got 2 mill and...
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Forum: Bioinformatics
07-10-2013, 05:17 AM
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Replies: 4
Views: 3,507
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Forum: Bioinformatics
07-09-2013, 03:22 PM
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Replies: 4
Views: 3,507
Bowtie2 mismatches option for small RNA mapping
I am using Bowtie2 to map small RNA reads (not microRNAs) to the genome. To account for allelic divergence, I need to set it to allow 1 or maybe even 2 mismatches. Is it possible to change that? I...
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Forum: Bioinformatics
07-01-2013, 09:04 AM
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Replies: 8
Views: 3,011
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Forum: Bioinformatics
07-01-2013, 08:59 AM
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Replies: 8
Views: 3,011
Sorry!
Here is the command I tried:
...
Sorry!
Here is the command I tried:
intersectbed -a Inputfile.bed -b compare.gff > output.bed
The first few lines of the resulting bed file look like this:
BAM◊‹%@HD VN:1.0 SO:unsorted...
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Forum: Bioinformatics
07-01-2013, 08:32 AM
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Replies: 8
Views: 3,011
I am getting a bizarre result from using the...
I am getting a bizarre result from using the intersectbed from bedtools. The output bed file contains strange characters and not the chromosomal coordinates as I expected.
Any suggestions?
Can...
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Forum: Bioinformatics
06-28-2013, 07:03 PM
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Replies: 45
Views: 14,732
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Forum: Bioinformatics
06-28-2013, 06:31 PM
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Replies: 45
Views: 14,732
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Forum: Bioinformatics
06-28-2013, 06:27 PM
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Replies: 45
Views: 14,732
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Forum: Bioinformatics
06-26-2013, 07:26 AM
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Replies: 8
Views: 3,011
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Forum: Bioinformatics
06-06-2013, 11:59 AM
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Replies: 16
Views: 3,874
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Forum: Bioinformatics
06-05-2013, 12:16 PM
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Replies: 16
Views: 3,874
Split SAM/BAM files into thousands of contigs
Hi,
I am new to bioinformatics and programming, so this might be too easy to tackle for some of you. I am working on a newly sequenced genome with thousands of contigs. I have Illumina sequence...
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Forum: Sample Prep / Library Generation
05-29-2013, 06:01 AM
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Replies: 35
Views: 22,322
This is the problem with companies in general....
This is the problem with companies in general. They sell kits with 'proprietary' components and won't disclose any other information.
15' does sound insufficient but maybe they are using a modified...
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Forum: Sample Prep / Library Generation
11-10-2011, 07:25 PM
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Replies: 35
Views: 22,322
What are your thoughts about Superscript II? I...
What are your thoughts about Superscript II? I have seen a few protocols which use Superscript II for first strand synthesis and I think there might be some advantage to it while there is already an...
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Forum: Sample Prep / Library Generation
11-09-2011, 12:51 PM
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Replies: 35
Views: 22,322
While we are discussing the usability of...
While we are discussing the usability of different reagents in preparing libraries, can anyone help me with my issue with Ampure beads. I just ordered them and wanted to test them for size retention...
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Forum: Sample Prep / Library Generation
11-02-2011, 09:51 AM
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Replies: 35
Views: 22,322
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Forum: Sample Prep / Library Generation
11-02-2011, 09:43 AM
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Replies: 35
Views: 22,322
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