User: caggtaagtat

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caggtaagtat370
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Posts by caggtaagtat

<prev • 137 results • page 1 of 14 • next >
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Answer: A: Genome index and Aligment with STAR- Rattus Norvegicus
... Hi, I would include the unplaced scaffolds for the generation of the indexing. They should be included in the toplevel file, but check check the documentation to be sure. The STAR command for alignment of your file looks good, however at the paramter `--outFileNamePrefix` a directoy is required, t ...
written 8 hours ago by caggtaagtat370
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Comment: C: Calculate CG content in a fastq file
... It is using all reads, so to speed things up you could potentially create a subset with 1 million reads, but I prefer running it using all availible reads. ...
written 9 hours ago by caggtaagtat370
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Comment: C: Calculate CG content in a fastq file
... Ok, that's what I thought :) I'll move my answer to the comment section ...
written 10 hours ago by caggtaagtat370
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Comment: A: Calculate CG content in a fastq file
... Hi, In case you don't know it already, I can recommend the tool FASTQC to you, which gives you the distribution of GC contents in your reads, distribution of read lengths, average Phred score per base and much more! Edit: In case you are looking at multiple FASTQ files at once, give the tool multiQ ...
written 11 hours ago by caggtaagtat370
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Comment: C: Why are file names deleted during submission of RNA-seq data to ENA, after disab
... Ok, I will do that, thank you! Edit: Access to ANNOTATE was restricted from the position of my PC, that's why I tried it via ENA. But I guess it's easier to just request clearing of the site from my institute. I was trying to upload RNA-seq data. ...
written 7 days ago by caggtaagtat370
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Why are file names deleted during submission of RNA-seq data to ENA, after disabling editor mode.
... Hi there, I'm trying to submit RNA-seq data to the ENA database. In order to upload the files, I have to insert the file name into the right spot of my submission spreedsheet. However, no matter how I write the path + name of the file into the slot, it gets deleted after disabling the editor mode. ...
fastq rna-seq ena written 7 days ago by caggtaagtat370
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Answer: A: Detecting antisense RNA in unstranded RNA-Seq data
... In unstranded RNA-Seq data, you generate reads, which represent the sense and anitsense of the sequenced RNA fragment, making it very difficult or even impossible to determine reads coming from sequencing of antisense RNA. One approach could be maybe, if you look at gapped reads, in case there are ...
written 8 days ago by caggtaagtat370
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Comment: C: Calculating significant variance of gene expression across multiple samples
... Thank you, I will try that! ...
written 14 days ago by caggtaagtat370
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Calculating significant variance of gene expression across multiple samples
... Hello, For my experiments, I want to calculate if a gene is significantly variable expressed across 40 biological similar samples in R. Until know, I assigned two random groups of the size of 20 and followed the DSEQ2 protocol for differential expression. However, 99.9% of the genes were asigned wi ...
R dge rna-seq dseq2 written 14 days ago by caggtaagtat370 • updated 14 days ago by ATpoint9.4k
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Comment: C: how to get a subset of vcf file for specific SNPs
... How would the file `file_listin_chr_and_positions` have to look like? I didn't find it in the manual. Maybe like this? 1 15342 15563 Y 1513212 1516246 Edit: Ok I thought I could select SNPs within a certain genomic range with that list, but that is not the case apparently. ...
written 20 days ago by caggtaagtat370

Latest awards to caggtaagtat

Scholar 5 weeks ago, created an answer that has been accepted. For A: Only 1% of reads are used as "input reads" in STAR
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: what do the headers of the rMATS output files mean?
Centurion 4 months ago, created 100 posts.
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: what do the headers of the rMATS output files mean?
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: what do the headers of the rMATS output files mean?
Scholar 6 months ago, created an answer that has been accepted. For A: Only 1% of reads are used as "input reads" in STAR
Supporter 8 months ago, voted at least 25 times.
Appreciated 8 months ago, created a post with more than 5 votes. For A: what do the headers of the rMATS output files mean?
Appreciated 9 months ago, created a post with more than 5 votes. For A: what do the headers of the rMATS output files mean?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: what do the headers of the rMATS output files mean?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: what do the headers of the rMATS output files mean?

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