User: BPors

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BPors40
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Posts by BPors

<prev • 23 results • page 1 of 3 • next >
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Counting Ribo-seq data on gene and transcript level?
... Hi, I am trying to count reads of Riboseq data - which ranges from 25 to 37 nt- and RNAseq data, on both gene and transcript level. For the gene level, I use Featurecounts : I am counting exons for RNA seq and CDSs for Riboseq data ( to count only coding RPFs) , and using their raw counts in downs ...
riboseq salmon featurecounts rna-seq written 4 months ago by BPors40
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Comment: C: Isoform level RNA-seq analyses
... I would like to keep the isoforms which are always being expressed regardless of the condition, so that I can use them in other analyses, for ex. checking how translation is effected etc. ...
written 4 months ago by BPors40
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Isoform level RNA-seq analyses
... Hi, I am considering to filter my transcripts based on expression, in that case, what are the options to choose the highly expressed isoform of each gene in a count matrix ( for example, salmon or FeatureCounts)? I found out that trinity has an option of isoform level filtering ( via its filter_lo ...
rna-seq isoform written 4 months ago by BPors40
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Comment: C: How to deal with clone genes?
... Sure. I attached a link to a screenshot in the question. I do not refer them as isoforms, as they do not share the same gene source, their transcripts are generated separately from their exons, which do not have a consistent description in between Ensembl genome versions. I could use protein codin ...
written 4 months ago by BPors40
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How to deal with clone genes?
... Hi, I am currently analysing RNA-seq data, and I realized in the GTF file (Ensembl v.96) which I use in mapping, there are ~19000 clone based (Ensembl) genes. Some of them share the exons with their 'parent' protein coding genes in terms of genomic locations. I am considering removing these clo ...
gene expresion isoforms rna-seq written 4 months ago by BPors40 • updated 4 months ago by h.mon28k
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How to compare the expression of a gene for some samples compared to the rest of the samples?
... I am trying to see the distribution of expressions of certain genes for certain patients, and want to compare them for the rest of the patients. For example, for 4 genes and 50 patients, some have values and some has no information for gene expression (empty): IDs Patient1 Patient2 ... ...
gene expression rna-seq written 20 months ago by BPors40
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Retrieving coverage image
... Hi! I am trying to visualize the coverage of my gene expression using IGV, and, I want to retrieve a high resolution and compact IGV image. Or, with the usage of any other tools. I found that I can use DEGseq however I am not very fluent with R, therefore have not try it yet. Do you have any sugge ...
next-gen igv coverage rna-seq expression written 2.2 years ago by BPors40
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Answer: A: Extract Sequence From Fasta File Using Ids From A Separate File
... If you had only the sequences in the example.txt instead of the identifiers, how would you grab the identifiers and their sequences? ( in this case, the purpose was retrieving the sequences with identifiers, what I am asking is retrieving headers and sequencers with known sequences ...
written 2.2 years ago by BPors40
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Comment: C: Searching for the common sequences in multiple (>2) fastq files
... True..Many thanks for the explanation. Would you suggest the usage of samtools ? ...
written 2.2 years ago by BPors40
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Comment: C: Searching for the common sequences in multiple (>2) fastq files
... Sure thing. What I meant is, my reads are 150 bp each in all fastq files, and I want to get the reads which are shared by other fastq files. The ultimate goal would be to grab the ones which are matching in more than 140 bps. However, I can put this threshold to 50 bp. So, if the read1 from fileA.fa ...
written 2.2 years ago by BPors40

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Popular Question 20 months ago, created a question with more than 1,000 views. For How to remove certain samples from SummarizedExperiment dataset? (BioConductor)

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