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Search: Posts Made By: Schelarina
Forum: Bioinformatics 01-02-2016, 08:19 AM
Replies: 2
Views: 1,969
Posted By Schelarina
hi, does mirdeep provide you with a list of...

hi,
does mirdeep provide you with a list of counts for each miRNA? if not, i guess it gives at least the genomic coordinates of your miRNAs, so you can make it as bedfile or gff file and use it to...
Forum: Bioinformatics 01-02-2016, 07:58 AM
Replies: 1
Views: 1,516
Posted By Schelarina
Normalization edgeR

Dear all,
I know there are thousands of posts regarding this topic.
HOW one can choose the best normalization method in edgeR??
I know that TMM is implemented in edgeR, but you can use other...
Forum: RNA Sequencing 01-02-2016, 06:47 AM
Replies: 4
Views: 3,825
Posted By Schelarina
Do you need CPM per each sample after TMM...

Do you need CPM per each sample after TMM normalization?
you could do something like this
cpm <- cpm(d, log=TRUE, lib.sizes=lib.sizes, normalized.lib.sizes = TRUE, prior.count=0.25)
if your cpm...
Forum: Bioinformatics 01-05-2015, 10:53 AM
Replies: 7
Views: 3,214
Posted By Schelarina
but I used unique mapping reads with bedtools...

but I used unique mapping reads with bedtools multicov
Forum: Bioinformatics 01-05-2015, 02:21 AM
Replies: 7
Views: 3,214
Posted By Schelarina
bedtools multicov and RPKM

I am calculating RPKM to make differential gene expression between two libraries.
First, I am extracting read counts for each gene interval using
bedtools multicov -bams file.bam -bed gene.gff3 >...
Forum: Bioinformatics 12-23-2014, 11:47 PM
Replies: 2
Views: 940
Posted By Schelarina
i checked and yes is a stranded protocol. all the...

i checked and yes is a stranded protocol. all the reads map on the opposite strand of mRNA. thank you very much!!
Forum: Bioinformatics 12-23-2014, 09:02 AM
Replies: 2
Views: 940
Posted By Schelarina
strange alignment results from RIPseq

Hello,
I did RIP-seq and used bwa to align the reads following this script

bwa index genome.fasta
bwa aln -n 0 file.sai genome.fasta file.fastq
bwa samse file.sam genome.fasta file.sai...
Forum: Bioinformatics 10-06-2014, 06:22 AM
Replies: 2
Views: 929
Posted By Schelarina
number of reads per region of interest

Hello,
I want to calculate the number of reads mapped to my reference in each gene, in the intergenic regions, in introns, in rRNA and tRNA.
I have bam and gff files. Which commands can I use?...
Forum: General 09-06-2014, 11:22 AM
Replies: 0
Views: 750
Posted By Schelarina
RNA secondary structure prediction

Hi,
you your opinion what is the best program to predict stem loop structure at wide level?
Forum: Bioinformatics 08-27-2014, 05:19 AM
Replies: 2
Views: 1,179
Posted By Schelarina
normalization bam file

Hello,
I have 3 smallRNA seq libraries mapped to the genome. I realized they are different in size. How do I normalize the libraries starting from bam files?
thanks
Forum: Bioinformatics 08-24-2014, 06:32 AM
Replies: 6
Views: 1,610
Posted By Schelarina
After I extracted the identical reads in a single...

After I extracted the identical reads in a single sequence from the bam file I aligned them again to the genome. When I use igv to visualize the alignment now all the sequences are mapping in sense...
Forum: Bioinformatics 08-20-2014, 08:11 AM
Replies: 6
Views: 1,610
Posted By Schelarina
thank you! it worked! can I do the same from a...

thank you! it worked!
can I do the same from a fastq file?
Forum: Bioinformatics 08-12-2014, 07:43 AM
Replies: 6
Views: 1,610
Posted By Schelarina
extracting identical reads from bam file

Hello,
I have an alignment file of smallRNAs in bam format.
How can I extact from this file all the identical reads in a single sequence but mantaining the reads count?
Thank you for the help!
Forum: Sample Prep / Library Generation 06-27-2014, 03:48 AM
Replies: 0
Views: 629
Posted By Schelarina
rip-seq library

Hello everybody,
I would like to make a RIP-Seq with Illumina. What would be the best kit to use? TruSeq Stranded mRNA Sample Preparation Kit ?
thanks
Forum: Illumina/Solexa 05-16-2014, 01:08 PM
Replies: 3
Views: 1,024
Posted By Schelarina
small RNAs are first processed as double stranded...

small RNAs are first processed as double stranded RNA and then dissociate and the sense strand is ligation competent. I am not 100% if the antisense strand which has P group at 3'end can also be...
Forum: Illumina/Solexa 05-16-2014, 04:08 AM
Replies: 3
Views: 1,024
Posted By Schelarina
small RNA sequencing

Hello,
TruesmallRNASeq kit is able to clone and sequence both strands of the small RNA?
Thanks
Forum: Sample Prep / Library Generation 05-05-2014, 02:33 AM
Replies: 2
Views: 2,598
Posted By Schelarina
mmm no answers yet.. it means that there is...

mmm no answers yet.. it means that there is something wrong or not clear?
Forum: Sample Prep / Library Generation 04-23-2014, 03:46 AM
Replies: 2
Views: 2,598
Posted By Schelarina
library preparation for Illumina sequencing

Hello everybody,
I have little experience with library preparation and Illumina sequencing :confused:. I just want to know if it makes sense what I am planning to do.
I have to generate multiplex...
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