User: mickey_95

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mickey_9510
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Posts by mickey_95

<prev • 26 results • page 1 of 3 • next >
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Comment: C: TSS metaprofile using Deeptools
... Here are the first lines of the gtf file: chr1 ensembl_havana gene 5588466 5606131 . + . gene_id "ENSMUSG00000025905"; gene_version "14"; gene_name "Oprk1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; chr1 ensembl_havana gene 6206197 6276648 . + . gene_id "ENSMUSG0000002590 ...
written 7 weeks ago by mickey_9510
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TSS metaprofile using Deeptools
... Hi, I am trying to use Deeptools' computeMatrix and plotHeatmap functions to create TSS-centered metaprofiles over all genes. Ultimately, I would like to apply some additional filters, e.g. protein-coding, non-overlapping TSSs, above a certain size. But for an initial trial, I decided to just filte ...
gtf deeptools computematrix metaprofile written 7 weeks ago by mickey_9510 • updated 6 weeks ago by zhuobaowen10
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Creating TxDB objects from different sources
... Hi! I have been trying to understand the confusing world of genome annotations with the goal of consistently using the same version throughout all analyses for one project. Initially I was using UCSC annotations by simply loading the corresponding library in R: library(TxDb.Mmusculus.UCSC.mm1 ...
genome annotation txdb biomart ensembl written 9 weeks ago by mickey_9510
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Comment: C: ATAC-seq coverage tracks using bamCoverage from Deeptools
... Ah, good to know. Thanks a lot! ...
written 3 months ago by mickey_9510
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Comment: C: ATAC-seq coverage tracks using bamCoverage from Deeptools
... Thanks a lot for your help! I will try this way of normalization then. I've also seen people downsample their BAM files to the read number of the lowest sample. What is your take on that? Speaking of normalization and varying library sizes, I have a rather general question: When pooling different s ...
written 3 months ago by mickey_9510
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ATAC-seq coverage tracks using bamCoverage from Deeptools
... Hello! I have recently started to use Deeptools for my ATAC-seq data analysis and would like to get some feedback on the conversion of the BAM files to bigwig coverage tracks. I am interested in looking at TSS metaprofiles using either all fragments or fragments of only certain sizes. **For an all ...
deeptools bigwig atac-seq bamcoverage written 3 months ago by mickey_9510
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Star alignment - AS and MD tags
... Hi, I am trying to understand some details about alignment of sequencing reads and the alignment tags that are included in the output files in SAM format. I am using the STAR aligner and have the following question: Will reads that map to multiple loci in the genome get assigned the same AS score ...
ngs alignment sam format star sam alignment tags written 4 months ago by mickey_9510
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Comment: C: Counting uniquely mapped reads - ambiguous results
... Ah, okay! Thanks for clarifying! ...
written 4 months ago by mickey_9510
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Comment: C: Counting uniquely mapped reads - ambiguous results
... Thanks for the quick response! Just to be sure I am understanding this correctly: If a read is mapping to multiple loci, the read with the best alignment score would be defined as primary alignment and all others would be secondary, correct? ...
written 4 months ago by mickey_9510
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Counting uniquely mapped reads - ambiguous results
... Hi, I have bam files aligned with Star, which according to the manual assigns a MAPQ score of 255 to all uniquely mapped reads. Using samtools view -c -q 255 myfile.bam I should obtain the number of uniquely mapped reads in my file. The same should be obtained using: samtools view -c -F ...
samtools view alignment samtools star mapping written 5 months ago by mickey_9510 • updated 5 months ago by ATpoint38k

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