User: rborges

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rborges50
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Posts by rborges

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Comment: C: Locating cells in a tSNE or Featureplot based on the defined threshold
... You can save the identities and go back to these if necessary by setting the identity again, or you can change the code to create identities based on the previous identity and the value of the gene, for example: Low_4, Low_3, etc [as done here:][1] I would still suggest saving the original identit ...
written 11 days ago by rborges50
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Comment: C: Locating cells in a tSNE or Featureplot based on the defined threshold
... What I would do is obtain the cells with the threshold you want and then set the identity name based on this, then I would do a tsne plot with these labels. I'm getting an error when I try to do a tsne plot with your data though, have you been able to do this? I'm not sure if you can label a feature ...
written 11 days ago by rborges50
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Answer: A: Locating cells in a tSNE or Featureplot based on the defined threshold
... Perhaps you can have a column $gene.threshold in object@data.info$gene.threshold where you give cells with a certain level of expression for the gene a distinct name. object<-SetIdent(object,ident.use=object@data.info$gene.threshold) Then once you plot Seurat should label and color by thes ...
written 11 days ago by rborges50
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BWA (mem, sampe, or aln) used in bam file
... I'm trying to figure out which version/type of bwa was used in three aligned bam files (sampe, mem or aln). Is there a way of figuring this out? I can't find information on this from where I downloaded the samples. Looking at the header, they say the following: samtools view -H file1.bam | g ...
bam bwa sequencing written 11 days ago by rborges50
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Comment: C: What Exactly Does A Read Represent?
... So if I have a depth of 100X in a certain region, which means this region is covered by 100 reads, does this mean that 100 different individual molecules from different cells in the sample stuck to the flow cell? Can one make this cell number assumption? ...
written 4.7 years ago by rborges50
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What Exactly Does A Read Represent?
... If I understand correctly, sequencing (Illumina) is done by amplifying molecules that have been fragmented and then synthesizing the corresponding strand to these amplified molecules and measuring fluorescence emitted during this synthesis. But then, what exactly does a read represent? Is it a conse ...
reads illumina sequencing written 4.7 years ago by rborges50 • updated 4.7 years ago by SES8.1k

Latest awards to rborges

Scholar 11 days ago, created an answer that has been accepted. For A: Locating cells in a tSNE or Featureplot based on the defined threshold
Popular Question 4.7 years ago, created a question with more than 1,000 views. For What Exactly Does A Read Represent?

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