User: pentium3-user

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Posts by pentium3-user

<prev • 12 results • page 1 of 2 • next >
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ClustalW alignment - Unexpected result
... Hi, I have two sequences >seq1 AAAAAAACCCCCCCCCCAAAAAAAAAAAAAAAAAAAAAAAAA >seq2 TTTTTTTTTTTTTTTTTTTCCCCCCCCCCTTTTTTTTTTTTT And I want to align them this way using clustalW AAAAAAA-------------------CCCCCCCCCCAAAAAAAAAAAAAAAAAAAAAAAAA------------- -------TTTTTTTTTTTT ...
alignment clustalw written 3 months ago by pentium3-user20
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Answer: A: RNASeq - low correlation between samples
... I finally found the problem(s). The main issue is the gene GlaA which is highly overexpressed in B36 (and also quite high in N402). If I take it out correlation gets as expected. I guess the MA cannot measure the gene correctly because of the saturation of the probes. Another issue was the read co ...
written 3 months ago by pentium3-user20
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Comment: C: RNA-seq: Explain STAR quantMode geneCounts values
... Sorry for digging in this old thread, but I have an understanding problem: 1). I have around 4000 genes (of 14000 overall) where $2 < $3 + $4 but I have no overlapping genes on the +/- strand. So how can this be explained? 2). For most reads I have $4 > $3, but for ~1000 $3 > $4. This I ...
written 4 months ago by pentium3-user20
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Comment: C: RNASeq - low correlation between samples
... Do you have any suggestions for any other quality control steps I can do? I'm writing my bachelor thesis with the goal to compare MA and RnaSeq. I want to find out if there are systematical biases in one/both methods, if there are classes of genes which one method suggests to be higher/lower expres ...
written 4 months ago by pentium3-user20
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What to do with corrupted lane files
... Hi, I have paired-end RNASeq data from 2 conditions with each 3 replicates from 2 lanes (lane04 and lane05). So I have 24 files. Unfortunately 3 files of lane04 are corrupted and cannot be restored. So what do you think is the best strategy? - Using only lane05 - Merging the healthy samples an ...
rna-seq lane written 4 months ago by pentium3-user20 • updated 4 months ago by genomax62k
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Comment: C: RNASeq - low correlation between samples
... N402 is a wild type of Aspergillus Niger. B36 a Glycoamylase-overproducer strain of Aspergillus Niger. For each strain 3 cultures were grown and for each culture a sample was taken for MA and one for RNASeq analysis. RNASeq data is strand-specific Paired End. NEBNext Ultra Directional RNA Librar ...
written 4 months ago by pentium3-user20
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Comment: C: RNASeq - low correlation between samples
... Hi, thanks for your reply. In the correlation plot I posted neither Microarray (MA) nor RNAseq data are log scaled (used ```2^exprs (results_ma)```). I also made a version with log scaled values. In this one RNASeq gets correlation of ~0.8 with RNASeq samples and ~0.6 to the MA samples. What let ...
written 4 months ago by pentium3-user20
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Comment: C: RNASeq - low correlation between samples
... Thanks for your reply. I just took the mean of the replicates. The correlation between the replicates is near to 1. The sequencing was processed by the same company with the same conditions for all samples. % of mapped reads is 86-89%. This is the code for read counting library(GenomicRange ...
written 4 months ago by pentium3-user20
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RNASeq - low correlation between samples
... Hi @ all, I'm comparing MicroArray based expression data with RNASeq expression data. For this I have data of two fungi strains, one named B36 the other named N402, each with 3 replicates. I observed quite low correlation between the the RNASeq samples. In the plot you can see the Pearson correla ...
R correlation rna-seq written 4 months ago by pentium3-user20
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Comment: C: [DeSeq2] some values in assay are negative
... Thank you very much, this works. So do I have to store the gene ids by my self in an extra vector or is there a better way how to keep the gene ids associated with the rows? In this example they don't have to drop the gene ids but I don't know why it's not working in my case: https://informatics.fa ...
written 10 months ago by pentium3-user20

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