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Forum: Bioinformatics 10-12-2015, 06:48 AM
Replies: 12
Views: 7,290
Posted By charlescoldroom
Thanks guys, I will check out the suggestions!

Thanks guys, I will check out the suggestions!
Forum: Bioinformatics 09-29-2015, 06:40 AM
Replies: 12
Views: 7,290
Posted By charlescoldroom
I am also interested to know about how to handle...

I am also interested to know about how to handle UMIs and remove duplicated reads based on UMIs.

I am using modified primers to have amplicon pools.

Which tools are there to mark/find UMIs and...
Forum: Sample Prep / Library Generation 01-10-2015, 10:38 AM
Replies: 0
Views: 1,277
Posted By charlescoldroom
Diploid genomic copies actually sequenced

Hi all, I would like to know if there is a way to calculate how many different genomes you sequence when you prepare amplicons from human gDNA. The goal is to do a power-calculation to understand how...
Forum: Bioinformatics 03-22-2014, 09:11 AM
Replies: 2
Views: 2,016
Posted By charlescoldroom
Thumbs up Hi dpryan, thanks a lot for the answer!...

Hi dpryan,

thanks a lot for the answer! pysam pileup does exactly what I needed, we are now using it to look up one position in a bam file and then output a list of all reads names and for each...
Forum: Bioinformatics 03-21-2014, 07:09 AM
Replies: 2
Views: 2,016
Posted By charlescoldroom
Extract reads with defined nucleotide at defined aligned position

Dear all,

I would like to extract from a BAM (or SAM) file the reads that contain a specified nucleotide at a specified location. E.g. I would like to extract all reads that have the reference...
Forum: Illumina/Solexa 06-18-2012, 12:28 AM
Replies: 7
Views: 3,219
Posted By charlescoldroom
Thanks for the answer luc! I will try a couple...

Thanks for the answer luc!
I will try a couple of samples in SSC just to see what happens, but for the rest where I can I will prepare new DNA.
Thanks again!
Forum: Illumina/Solexa 06-15-2012, 12:23 PM
Replies: 7
Views: 3,219
Posted By charlescoldroom
DNA quantitation & library preparation problem

Hello,
I am completely new to (deep) sequencing.

The project I am starting involves deep sequencing of SeqCap-enriched sequencing using the HiSeq sequencer.

I have a question...
To extract...
Forum: Introductions 06-15-2012, 12:17 PM
Replies: 0
Views: 661
Posted By charlescoldroom
Hello everybody!

Hello!
I am a biochemist, starting fresh in the new (to me) world of deep sequencing and bioinformatics!
Great community here, I have already learned quite a bit! :)
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