User: anikb

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anikb10
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Posts by anikb

<prev • 12 results • page 1 of 2 • next >
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Comment: C: ERCC Spike-in analysis without using any packages
... Thanks for the recommendation! How did you get to install the RUVSeq package? I keep getting non-zero status for ‘Matrix’, ‘RcppArmadillo’, ‘rgl’ packages. I updated R/Rstudio to the latest version (because that's what it was complaining about , initially). Still not working: > configure: error: ...
written 10 months ago by anikb10
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Comment: C: ERCC Spike-in analysis without using any packages
... Thank you, Charles, for your reply! I had read that post of yours earlier, and I am actually taking those tips into consideration for my DEG analysis. Since I already have ERCC spiked-in data, I also wanted to compute DEG with ERCC into account and see what the differences would be in final results. ...
written 10 months ago by anikb10
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ERCC Spike-in analysis without using any packages
... Can anyone please help me understand how to perform ERCC spike-in analysis and interpret the results? I know there are some packages to do it, I used erccdashboard but I keep getting a label error, so I was thinking if I could do it on Python without using any ercc analysis packages. So, basically I ...
ercc spike-in rna-seq written 10 months ago by anikb10 • updated 10 months ago by Charles Warden7.5k
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Comment: C: Cutadapt for paired end RRBS data
... Hi Devon, Just a follow up on the last question. I trimmed the files and ran bismark with default options as below: 1. Genome preparation: `bismark_genome_preparation --verbose hg38_gencode` 2. Alignment: `bismark reference_genome -1 Read_1.fq -2 Read_2.fq` The M-bias plots look like these (belo ...
written 19 months ago by anikb10
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Comment: C: Cutadapt for paired end RRBS data
... Thanks a bunch, that really helped! ...
written 19 months ago by anikb10
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Comment: C: Cutadapt for paired end RRBS data
... 1. Hmm, ok. Thank you for your answer! So I will not mess with the repaired bases at this point then and take care of it after creating the M-bias plot. I might have to use Bismark, since that's what is available on our cluster, and it has both the features that you mentioned above(3,4) . Is bwa-met ...
written 19 months ago by anikb10
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Cutadapt for paired end RRBS data
... Hi all, I have just started working with RRBS data, and I am having issue understanding the data and need to understand how to trim adapter sequences. This is probably a very naive question, but any help would be appreciated. I am trying to trim paired-end RRBS data using Cutadapt. (I am aware of ...
trimming rrbs cutadapt written 19 months ago by anikb10 • updated 19 months ago by Devon Ryan93k
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Comment: C: STAR output - high multi-mapping, low alignment (human)
... I see. Thank you, h.mon. This is extremely helpful! ...
written 19 months ago by anikb10
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Comment: C: STAR output - high multi-mapping, low alignment (human)
... Oh I meant to say that "80-90% unique alignment is expected for human data" - that's what I came across in multiple forums. Thank you for your answer. I will just proceed with the analysis, but will perform PCA plot to see how these samples cluster like h.mon suggested. ...
written 19 months ago by anikb10
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Comment: C: STAR output - high multi-mapping, low alignment (human)
... Thank you very much! Since this is one of my first couple posts, I overlooked the formatting. Apologies. I will use the formatting bar from next time. ...
written 19 months ago by anikb10

Latest awards to anikb

Popular Question 10 months ago, created a question with more than 1,000 views. For STAR output - high multi-mapping, low alignment (human)
Popular Question 19 months ago, created a question with more than 1,000 views. For STAR output - high multi-mapping, low alignment (human)

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