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Forum: Sample Prep / Library Generation 09-25-2013, 11:48 PM
Replies: 3
Views: 3,564
Posted By visserm
Hi JenMar I haven't used the Pippin in a...

Hi JenMar

I haven't used the Pippin in a while and in the end started using PAGE (I do not have easy access to the machine anymore). In order to avoid selecting libraries without an insert I set...
Forum: Bioinformatics 07-25-2013, 02:58 AM
Replies: 23
Views: 26,703
Posted By visserm
Hi Michael, Is the shrunken log fold change...

Hi Michael,
Is the shrunken log fold change also applied in DESeq2 v 1.0.17?
Forum: Bioinformatics 07-10-2013, 05:15 AM
Replies: 6
Views: 3,743
Posted By visserm
Hi Holly I used miRanalyzer for analyzing...

Hi Holly

I used miRanalyzer for analyzing known miRNA. As you know, miRanlyzer makes use of the bowtie indexed mature and hairpin files (the fasta files they got from mirBase). You can also index...
Forum: Bioinformatics 07-10-2013, 04:38 AM
Replies: 6
Views: 3,743
Posted By visserm
Hi Holly Have you added 25 G's after your...

Hi Holly
Have you added 25 G's after your mature miRNA sequences before you indexed them with Bowtie?
Marike
Forum: Bioinformatics 02-07-2013, 05:09 AM
Replies: 11
Views: 42,219
Posted By visserm
Hi there, I also have a problem converting...

Hi there,

I also have a problem converting SAM to BAM with samtools. I used the command...

samtools view -bS file.sam > file.bam

and got the following error...

[samopen] SAM header is...
Forum: Sample Prep / Library Generation 01-05-2012, 12:18 AM
Replies: 3
Views: 3,564
Posted By visserm
PippinPrep for TruSeq small RNA library selection

Hi all,

I want to use the PippinPrep for size selection of my TruSeq small RNA libraries. In the TruSeq kit they give the specs for selection an a polyacrylamide gel. They however compensate...
Forum: Introductions 01-05-2012, 12:00 AM
Replies: 373
Views: 140,611
Posted By visserm
Hi everyone, I am a PhD student from South...

Hi everyone,
I am a PhD student from South Africa, and are a newbie working on small RNA profiling.
Marike
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