User: elsoja

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elsoja120
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Posts by elsoja

<prev • 34 results • page 1 of 4 • next >
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Comment: C: Bowtie2 and BWA-MEM giving very different results in metagenomic data
... I don't think this is the main source of the problem (even though it certainly contributes to it). When I use local alignment the % of mapped reads goes from 30.15% to 42.56%. It's a large increase, but it's still far from BWA-MEM. 182783328 + 0 in total (QC-passed reads + QC-failed reads) ...
written 8 months ago by elsoja120
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Comment: C: Bowtie2 and BWA-MEM giving very different results in metagenomic data
... I think you are right. I knew that BWA-MEM uses soft-clipping, but I've never checked whether that's the case for Bowtie2. Indeed, [Bowtie2 is end-to-end][1]. I'll do a test and post the result here. [1]: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#end-to-end-alignment-versus-local-al ...
written 8 months ago by elsoja120
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Comment: C: Bowtie2 and BWA-MEM giving very different results in metagenomic data
... Sure! They were both executed with the default parameters. bwa mem -t 80 bwa_index reads_1.fastq.gz reads_2.fastq.gz | samtools view -bS - > bwa.bam bowtie2 --threads 80 -x bowtie_index -1 reads_1.fastq.gz -2 reads_2.fastq.gz | samtools view -bS - > bowtie2.bam ...
written 8 months ago by elsoja120
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Bowtie2 and BWA-MEM giving very different results in metagenomic data
... I've assembled a metagenome using MEGAHIT and begun testing different mapping options to perform the binning of the contigs. However, I've noticed that Bowtie2 and BWA-MEM had very different mapping rates to the metagenome: **Bowtie2:** 182783328 + 0 in total (QC-passed reads + QC-failed reads ...
metagenomics alignment bowtie genomics bwa written 8 months ago by elsoja120
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Comment: C: RNA-Seq quantification of a heterozygous individual with a short deletion
... Thank you, Lior! That's what I'm doing right now. I was apprehensive in introducing more ambiguity into a locus in which the individual isoform expression is a relevant information. However, it seems like the EM gave me results that are very close to what I was expecting. ...
written 10 months ago by elsoja120
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Comment: C: Can I filter mRNA from bulk RNA-seq reads?
... I'm very sorry! I read your question wrong! I don't think that there's a method that can identify if a read is from a mRNA. I can suggest two alternatives: - If the organism that you are working with has a reference annonation, you can map the reads to the mRNA sequences (using BWA or Bowtie) and t ...
written 10 months ago by elsoja120
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RNA-Seq quantification of a heterozygous individual with a short deletion
... I'm quantifying transcript expression of RNA-Seq data collected from a mouse that is heterozygous in a given locus. One of the alleles is wild-type while the other has a deletion (~20bp). Should I take any special care when quantifying those samples or can I use Salmon/Kallisto/RSEM with a standard ...
rna-seq written 10 months ago by elsoja120 • updated 10 months ago by Lior Pachter530
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Comment: A: Can I filter mRNA from bulk RNA-seq reads?
... Yes. You can use SortMeRNA for that. https://bioinfo.lifl.fr/RNA/sortmerna/ ...
written 10 months ago by elsoja120
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Comment: C: Is it possible to detect lncRNA in a de novo assembled genome?
... There are some tools that can distinguish between lncRNAs and mRNAs even if the transcript sequence is incomplete (as you would expect in a de novo assembly). You can check Figure 5 [here][1]. [1]: https://www.biorxiv.org/content/10.1101/620880v1.full ...
written 10 months ago by elsoja120
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Answer: A: Currently what is the best tool for long non-coding RNA annotation? Is FEELnc a
... (Update to the thread) FEELnc is still a great choice, but some other great lncRNA annotation tools were published recently. - [RNAsamba][1] (disclaimer: I'm the author of this tool) - [lncFinder][2] - [LncADeep][3] [1]: https://rnasamba.lge.ibi.unicamp.br/ [2]: http://bmbl.sdstate.edu/lncfi ...
written 10 months ago by elsoja120

Latest awards to elsoja

Popular Question 4 weeks ago, created a question with more than 1,000 views. For DE analysis of low-expression transcripts
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Popular Question 8 months ago, created a question with more than 1,000 views. For Transforming stranded RNA-Seq libraries in unstranded
Popular Question 13 months ago, created a question with more than 1,000 views. For Transforming stranded RNA-Seq libraries in unstranded
Popular Question 14 months ago, created a question with more than 1,000 views. For How to create 'gene' and 'transcript' entries in a GTF containing only exons
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Microbial diversity analysis using whole-genome metagenomic data
Popular Question 2.9 years ago, created a question with more than 1,000 views. For How to create 'gene' and 'transcript' entries in a GTF containing only exons
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Insert size in RNA-Seq library

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