User: debitboro

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debitboro110
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Posts by debitboro

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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 7 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 7 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 7 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 7 months ago by debitboro110 • updated 7 months ago by RamRS19k
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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 7 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 7 months ago by debitboro110 • updated 7 months ago by Friederike2.3k
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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 7 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 7 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 7 months ago by debitboro110 • updated 4 months ago by caggtaagtat380
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Questions about STAR and Bowtie (not Bowtie2) mapping
... Hi all, I want to perform an alignment of short reads against a reference genome (human genome from Ensembl). For that I've used STAR, and Bowtie (not Bowtie2). I've some questions about that. 1- I've used STAR by setting the more important parameters as follows: --outFilterScoreMinOverLread ...
bowtie star uniquely mapped reads rna-seq written 8 months ago by debitboro110 • updated 8 months ago by RamRS19k

Latest awards to debitboro

Scholar 12 days ago, created an answer that has been accepted. For A: Bug in RUV spike-in normalization?
Scholar 12 days ago, created an answer that has been accepted. For A: Bug in RUV spike-in normalization?
Popular Question 26 days ago, created a question with more than 1,000 views. For Gene length table from gtf file for rpkm() function
Popular Question 26 days ago, created a question with more than 1,000 views. For Cufflinks: exceeded memory limit (31836604 > 31457280), being killed
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Gene length table from gtf file for rpkm() function
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Gene length table from gtf file for rpkm() function
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Cufflinks: exceeded memory limit (31836604 > 31457280), being killed
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Gene length table from gtf file for rpkm() function
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Gene length table from gtf file for rpkm() function
Popular Question 12 weeks 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
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Popular Question 15 months ago, created a question with more than 1,000 views. For Cleaning RNA-Seq data from rRNA
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Popular Question 21 months ago, created a question with more than 1,000 views. For Cleaning RNA-Seq data from rRNA

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