User: debitboro

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debitboro110
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Posts by debitboro

<prev • 76 results • page 1 of 8 • next >
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positive and negative Fold Change glmLRT test
... Dear Biostars, I've a RNAseq counts dataset of 32 samples belonging to two groups: group1 (16 samples) and group2 (16 samples). Each group contains 2 subgroups: subgroup1 (8 samples), and subgroup2 (8 samples). Now, by using glmLRT test I want to find deferentially expressed genes between subgroups ...
log2fc glmlrt rna-seq differential expression written 10 weeks ago by debitboro110
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Comment: C: short RNA reads alignment
... I mapped my reads against Human genome (Homo_sapiens.GRCh38.dna.primary_assembly.fa). Did you mean my reads are contaminated by rRNA sequences ? ...
written 14 months ago by debitboro110
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Comment: C: short RNA reads alignment
... Hi genomax, Thank you for your suggestion, I've used BBMap with the values of parameters as you suggested, and I got the following results (I used another sample different from the one used for STAR alignment, but both of them are generated using the same protocol): ------------------ Res ...
written 14 months ago by debitboro110
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Comment: C: All my reads fall in intergenic regions ?
... Since the length of my reads is distributed between 22-50 nt, I think it is clear I got a high rate of multiple mapped reads. A very short read of 25 nt will get a higher number of multiple aligned locations on the genome than a read of a higher length. I am right ? ...
written 14 months ago by debitboro110
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Comment: C: All my reads fall in intergenic regions ?
... >80% rRNA even if rRNAs have been removed during the experiment with rRNA depletion kit ? ...
written 14 months ago by debitboro110 • updated 14 months ago by RamRS22k
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Comment: C: All my reads fall in intergenic regions ?
... It is total RNAseq experiment. The sequencing has been done on degraded RNA samples (single-end) and with a particular library preparation protocol, that is why I got very short RNAseq reads. We don't target any class of RNAs. ...
written 14 months ago by debitboro110
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All my reads fall in intergenic regions ?
... Hi biostars, I've performed an alignment using Bowtie on small RNAseq reads (22-50 nt) from total RNA-Seq sequencing experiment. I got almost 90% of multiple mapped reads. Then, I counted the reads per biotype (gtf file from Ensembl) using mmquant program (which is designed for counting tasks in th ...
intergenic regions rna-seq count per biotype written 14 months ago by debitboro110 • updated 14 months ago by Friederike4.5k
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Answer: A: How to calculate distribution of mapped read over classes of RNA?
... If you get a high rate of multiple mapped reads and a low rate of uniquely mapped reads then the process to find the percentage of mapped reads by biotype will be slightly difficult. A classical way to do that is to perform the mapping and then counting the number of reads per features (featureCount ...
written 14 months ago by debitboro110
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Answer: A: Precision Medicine Bioinformatics: From raw genome and transcriptome data to cli
... Precision Medicine Bioinformatics: From raw genome and transcriptome data to clinical interpretation (PMBI01) 29 October 2018 - 2 November 2018 https://www.prinformatics.com/course/precision-medicine-bioinformatics-from-raw-genome-and-transcriptome-data-to-clinical-interpretation-pmbi01/ ...
written 15 months ago by debitboro110
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sortMeRNA before or after adapters trimming ?
... Hi Biostars community, Shall I use sortMeRNA before or after poly(A) tails removal and/or adapters trimming ? Thanks ...
rrna sortmerna rna-seq written 15 months ago by debitboro110 • updated 12 months ago by caggtaagtat650

Latest awards to debitboro

Popular Question 3 months ago, created a question with more than 1,000 views. For Cufflinks: exceeded memory limit (31836604 > 31457280), being killed
Popular Question 3 months ago, created a question with more than 1,000 views. For Tophat2 error when mapping using -G option
Popular Question 3 months ago, created a question with more than 1,000 views. For RNA-Seq Mapping and bowtie2 indexing
Great Question 4 months ago, created a question with more than 5,000 views. For Cleaning RNA-Seq data from rRNA
Popular Question 5 months ago, created a question with more than 1,000 views. For Gene length table from gtf file for rpkm() function
Popular Question 5 months ago, created a question with more than 1,000 views. For Gene length table from gtf file for rpkm() function
Popular Question 6 months ago, created a question with more than 1,000 views. For Gene length table from gtf file for rpkm() function
Scholar 7 months ago, created an answer that has been accepted. For A: Bug in RUV spike-in normalization?
Scholar 7 months ago, created an answer that has been accepted. For A: Bug in RUV spike-in normalization?
Popular Question 8 months ago, created a question with more than 1,000 views. For Gene length table from gtf file for rpkm() function
Popular Question 8 months ago, created a question with more than 1,000 views. For Cufflinks: exceeded memory limit (31836604 > 31457280), being killed
Popular Question 8 months ago, created a question with more than 1,000 views. For Gene length table from gtf file for rpkm() function
Popular Question 8 months ago, created a question with more than 1,000 views. For Gene length table from gtf file for rpkm() function
Popular Question 8 months ago, created a question with more than 1,000 views. For Cufflinks: exceeded memory limit (31836604 > 31457280), being killed
Popular Question 9 months ago, created a question with more than 1,000 views. For Gene length table from gtf file for rpkm() function
Popular Question 9 months ago, created a question with more than 1,000 views. For Gene length table from gtf file for rpkm() function
Popular Question 10 months ago, created a question with more than 1,000 views. For Gene length table from gtf file for rpkm() function
Popular Question 14 months ago, created a question with more than 1,000 views. For Gene length table from gtf file for rpkm() function
Popular Question 14 months ago, created a question with more than 1,000 views. For RNA-Seq for DE analysis
Popular Question 14 months ago, created a question with more than 1,000 views. For Using of WGCNA to identify modules in Normal/Tumor tissues
Popular Question 14 months ago, created a question with more than 1,000 views. For Cleaning RNA-Seq data from rRNA
Great Question 14 months ago, created a question with more than 5,000 views. For Cleaning RNA-Seq data from rRNA
Popular Question 18 months ago, created a question with more than 1,000 views. For Cleaning RNA-Seq data from rRNA
Popular Question 18 months ago, created a question with more than 1,000 views. For RNA-Seq for DE analysis
Popular Question 18 months ago, created a question with more than 1,000 views. For Technical and Biological replicates

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