User: star

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star70
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Posts by star

<prev • 66 results • page 1 of 7 • next >
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Comment: C: bowtie2-align exited with value 139 ?
... @ jrj.healey,Thanks for reply, I put the commands. ...
written 15 days ago by star70
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bowtie2-align exited with value 139 ?
... I have some data and I like to run bowtie2 for them, its version is 2.3.4.3. when I run it as loop for all samples I have faced with `Segmentation fault (core dumped) (ERR): bowtie2-align exited with value 139`, error, but when I run it for each sample separately it works. is there any solution for ...
software error bowtie2 alignment chip-seq rna-seq written 15 days ago by star70
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Comment: C: merge Fastq or Bam file?
... Thanks for reply, but in that question my problem was related to technical and biological replicate, but here is about deference between merging bam and fastq files. I like to know is it impact on downstream results. ...
written 16 days ago by star70
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(Closed) merge Fastq or Bam file?
... I have three technical replicates from RNA seq data, I like to merge them together. I would like to know is there any difference if I merge them after aligning (after aligning each one separately) as .bam file or I can do that before aligning when I have Fastq file then run alignment? ...
alignment chip-seq rna-seq written 16 days ago by star70
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How to extract mapping features of multiple samples in one output?
... I have a multiple samples and I run mapping with Bowtie2 for them and now I have .bam files. I have tried to run Multiqc to see how is mapping rate, duplication rate and other features but It did not work with bowtie output I think. I would like to know is there any graphical program like Multiqc f ...
bowtie2 chip-seq mapping multiqc rna-seq written 20 days ago by star70 • updated 20 days ago by h.mon21k
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(Closed) aligning using bowtie2?
... I am doing aligning with bowtie2 and just need reads that aligned exactly 1 time. so I have performed 2 ways: but I am not sure whether the first one is correct or not, while most of literature used the second one? 1= bowtie2 --very-sensitive --score-min C,0,0 --> that number of aligned exactly ...
genome R alignment chip-seq rna-seq written 3 months ago by star70
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Comment: C: shift direction in ATAC/DNase data?
... Thanks for your reply! is it necessary to use `--nomodel` for PE reads, I mean just use `-f BAMPE`. How about when there is SE reads, shall we use `--nomodel --shift -100 --extsize 200`? ...
written 3 months ago by star70
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shift direction in ATAC/DNase data?
... I have two set of data about ATAC-seq and DNase-seq and I like to perform peak calling using MACS2, but I found that there are some differences in shift size (plus or minus direction). I like to know which one is better for either ATAC-seq or DNase-seq `(e.g. --nomodel --shift -100 --extsize 200 or ...
macs2 chip-seq atac-seq dnase-seq written 3 months ago by star70
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Can be merged biological replicates?
... Can we merge/ combine biological replicates from same sample together in ChIP-seq / ATAC-seq data when we want to do peak calling (or like RNA seq we should process each replicate separately)? because I am seeing in some papers, the data were merged for peak calling and some where else processed sep ...
chip-seq macs2 peak-calling atac-seq rna-seq written 3 months ago by star70 • updated 10 weeks ago by ZZzzzzhong120
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why is there still duplication after extracting aligned read exactly 1 time?
... I have some ChIP seq data that I have done aligning with bowtie2 --very-sensitive --score-min C,0,0 and then extract aligned read exactly 1 time and then remove duplication using Picard tools. I like to know why we have still duplication while I have extracted only aligned read exactly 1 time? T ...
duplicate alignment chip-seq samtools rna-seq written 3 months ago by star70 • updated 3 months ago by ATpoint11k

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