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Search: Posts Made By: Anastaziel
Forum: Bioinformatics 10-04-2019, 12:10 PM
Replies: 1
Views: 617
Posted By Anastaziel
I think I fixed it. The adapter for my files...

I think I fixed it. The adapter for my files should be TGGAATTCTCGGGTGCCAAGG. From what-sequences-do-i-use-for-adapter-trimming...
Forum: Bioinformatics 10-04-2019, 07:44 AM
Replies: 1
Views: 617
Posted By Anastaziel
miRDeep2 and adapter trimming

I am trying to align a miRNA-seq FASTQ file using the mapper.pl from miRDeep2 but I am not having any luck.

The reads in the FASTQ file are ~50bp.

I am not sure where my mistake is as I get...
Forum: Bioinformatics 04-04-2017, 07:37 AM
Replies: 0
Views: 1,980
Posted By Anastaziel
Question Fusion reads in BAM

I have BAM files which were run with tophat and --fusion-search --fusion-min-dist 1000000 --fusion-read-mismatches 2 --fusion-multireads 1 --fusion-multipairs 1 --fusion-anchor-length 10 -p 14.

I...
Forum: Bioinformatics 02-12-2016, 01:53 AM
Replies: 4
Views: 1,295
Posted By Anastaziel
I was able to fix my problem. I was using a wrong...

I was able to fix my problem. I was using a wrong test case and my model was becoming too big. Using the example from glment.pdf (https://cran.r-project.org/web/packages/glmnet/glmnet.pdf) fixes the...
Forum: Bioinformatics 02-11-2016, 03:50 PM
Replies: 4
Views: 1,295
Posted By Anastaziel
I am sorry, I did not know that it is against the...

I am sorry, I did not know that it is against the rules to post in multiple forums the same question. Not to make another post on this: I will mention if on the other forum the question in answered....
Forum: Bioinformatics 02-11-2016, 03:14 PM
Replies: 4
Views: 1,295
Posted By Anastaziel
A problem with Elastic net + Cox regression

I was trying to perform elastic net + cox regression in R using the glmnet package. The problem is that my data is around 100 individuals with ~100k features and the model is too big for R to store...
Forum: Bioinformatics 06-28-2015, 06:59 AM
Replies: 1
Views: 1,549
Posted By Anastaziel
Birdseed to VCF

I have a lot of birdseed files (from TCGA) and I need to convert them to vcf format. Anyone know of a good script I can use?
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