User: Ming

gravatar for Ming
Ming30
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30
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New User
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Last seen:
3 weeks, 1 day ago
Joined:
8 months ago
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s**************@hotmail.com

Posts by Ming

<prev • 31 results • page 1 of 4 • next >
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Calculating relative abundance of taxonomies from BLAST output
... Dear All, I am trying to calculate the relative abundance of taxonomies derived from a BLAST output. I have observed that one predicted gen/qseqid has multiple matches to the subject/sseqid. This will affect the relative abundance as the relative abundance will get inflated. How do I select the bes ...
blast written 29 days ago by Ming30 • updated 29 days ago by 5heikki8.4k
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Differential abundance analysis of two samples with only a single replicate
... Dear All, I am trying to perform a differential abundance analysis of two sets of samples (Samples A and B), in which they approximately share 20 OTUs. However, I only have 2 replicates for Sample A, and 1 replicate for sample B. I will like to find out which OTUs are more quantitatively abunda ...
deseq2 written 4 weeks ago by Ming30
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How do I look for shared OTUs in an abundance matrix?
... Dear all, Let's assume I have an abundance matrix that looks like this: SampleA SampleB SampleC OTU1 5 6 0 OTU2 3 1 2 OTU3 1 0 1 OTU4 0 0 ...
R venn diagram written 6 weeks ago by Ming30 • updated 6 weeks ago by zx87547.8k
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Comment: C: No color observed in Colour Key of HeatMap.2
... Dear @SMK, how would you change the code? ...
written 6 weeks ago by Ming30
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Comment: C: No color observed in Colour Key of HeatMap.2
... Dear @benformatics, what other kind of information will you like? ...
written 6 weeks ago by Ming30
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No color observed in Colour Key of HeatMap.2
... Dear All, I am trying to plot a heatmap with the heatmap.2 function, but I am not getting any color on my Color Key. The following are my code: col1 <- colorRampPalette(c("green", "black", "red"))(499) > col_breaks = c(seq(0, 0.002, length = 50), > seq(0.0021, ...
R heatmap.2 written 7 weeks ago by Ming30 • updated 7 weeks ago by ATpoint19k
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Normalization with BBnorm
... Hello All, I am trying to perform a co-assembly from 2 samples that have been sequenced across two lanes of Hi-Seq, but I am not able to do so because of computational limitation problems. I have came across BBnorm where it is possible to perform digital normalization. How do I determine the medi ...
bbnorm written 12 weeks ago by Ming30
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BLAST qcov equals to 0
... Hello All, I just performed a blastn, and I have some alignment returning qcovs = 0. I am not sure how this is possible because the alignment reports a pident and a bitscore for that alignment. For instance: qseqid sseqid pident bitscore evalue qcovs qcovhsp length k127_1554010 ref|NZ_ ...
blast written 3 months ago by Ming30 • updated 6 weeks ago by h.mon26k
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Comment: C: Extracting the aligned sequence from a BLAST output in a multi-fasta file
... @flogin, thank you very much for pushing me in the correct direction! ...
written 3 months ago by Ming30
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Extracting the aligned sequence from a BLAST output in a multi-fasta file
... Dear All, I am trying to extract the aligned sequences from my query search from a BLAST output in a single multi-fasta file. How do I go about doing so? Thank you in advanced. ...
blast written 3 months ago by Ming30 • updated 3 months ago by flogin140

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