User: elsoja

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elsoja120
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Posts by elsoja

<prev • 36 results • page 1 of 4 • next >
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Re-evaluating SAM/BAM bitflags after modifying the file
... Hey all, I'm using pysam to filter a BAM file based on alignment identity (which I'm calculating from the NM tag). Because the filtering is performed on individual reads, and not reads pairs, this can lead to misleading flags in the resulting BAM file. For example, lets suppose that both reads fro ...
alignment written 5 weeks ago by elsoja120
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Comment: C: Bowtie2 and BWA-MEM giving very different results in metagenomic data
... Because I didn't have a metagenome to map to :) ...
written 5 weeks ago by elsoja120
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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 12 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 12 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 12 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 12 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 13 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 13 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 13 months ago by elsoja120 • updated 13 months ago by Lior Pachter540
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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 13 months ago by elsoja120

Latest awards to elsoja

Popular Question 4 months ago, created a question with more than 1,000 views. For DE analysis of low-expression transcripts
Great Question 7 months ago, created a question with more than 5,000 views. For How to create 'gene' and 'transcript' entries in a GTF containing only exons
Popular Question 11 months ago, created a question with more than 1,000 views. For Transforming stranded RNA-Seq libraries in unstranded
Popular Question 16 months ago, created a question with more than 1,000 views. For Transforming stranded RNA-Seq libraries in unstranded
Popular Question 17 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 2.5 years ago, created a question with more than 1,000 views. For Microbial diversity analysis using whole-genome metagenomic data
Popular Question 3.2 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 3.2 years ago, created a question with more than 1,000 views. For Insert size in RNA-Seq library

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