User: Macspider

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Macspider1.6k
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Vienna - BOKU
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Posts by Macspider

<prev • 343 results • page 1 of 35 • next >
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Comment: C: converting genotype file to vcf
... You mean converting this genotype file to the VCF-formatted *genotype*, right? Because if you want a whole VCF line, you miss some information! EDIT: individual 4 has only 1 line! ...
written 10 days ago by Macspider1.6k
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Comment: C: SAM Flags for illumina paired-end reads mapped on transcriptome
... 8 weeks later, the problem rises again in a different form: would you keep 83 and 163? they are the ONLY flags I have after filtering. I find it suspicious because my reads should face each other, they shouldn't map as mate pairs. ...
written 15 days ago by Macspider1.6k
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Comment: C: Unusual AF data (I think)
... Could you add axes labels also on the plots shown, to help readers? ...
written 17 days ago by Macspider1.6k
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Comment: C: RPKM documentation is needed!
... I think you should read this (as a side note): https://liorpachter.wordpress.com/tag/rpkm/ ...
written 4 weeks ago by Macspider1.6k
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Whole-transcriptome RNASeq data of RNA-i engineered organism
... I am working with an organism that has been engineered with a transgene to perform RNA-interference. I have whole-transcriptome RNASeq data for this organism. Now: - I expect RNA reads coming from the transgene in my sample - I also expect RNA reads from the downregulated transcript, but less th ...
transgene rnai sequencing rna-seq transcriptome written 5 weeks ago by Macspider1.6k
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Comment: C: Unexpected RNASeq result in shRNA experiment
... > The remaining fragments still can be there longer than we thought and are aligned and counted. I know that 2.4 years have passed by since this comment, but: do you have a literature reference to cite for this sentence? I desperately need one and can't find it. I refuse to cite a biostars post ...
written 5 weeks ago by Macspider1.6k
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Comment: C: denovo assembly of unmapped reads
... There is no such thing as "better values". Parameters have to be chosen according to your data. From the manual: > **--score-min :** Sets a function governing the minimum alignment score needed for an alignment to be onsidered "valid" (i.e. good enough to report). **This is a function of read ...
written 5 weeks ago by Macspider1.6k
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Comment: C: denovo assembly of unmapped reads
... To the updated question: your mismatch penalty seems to be quite high compared to what the threshold for alignment scores is if you don't touch the scoring function. Increasing penalties for gaps and mismatches obviously results in more unmapped reads. ...
written 5 weeks ago by Macspider1.6k
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Comment: C: denovo assembly of unmapped reads
... Good point, I gave you my answer below but it holds only as long as @genomax's point is fulfilled. ...
written 5 weeks ago by Macspider1.6k
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Answer: A: denovo assembly of unmapped reads
... I think the best way to proceed would be to: - map your RNASeq reads against the wheat genome with stringent criteria with hisat2 or bowtie2 using: > --mp , max and min penalties for mismatch; lower qual = lower penalty <6,2> > --rdg , read gap open, extend penalties ( ...
written 5 weeks ago by Macspider1.6k

Latest awards to Macspider

Popular Question 10 days ago, created a question with more than 1,000 views. For Remove duplicates from reads: best practices?
Appreciated 17 days ago, created a post with more than 5 votes. For Best way to compare two samples in a VCF file
Scholar 9 weeks ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: How to convert .bed file to .juncs file using Tophat?
Scholar 10 weeks ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Popular Question 3 months ago, created a question with more than 1,000 views. For Best way to compare two samples in a VCF file
Student 6 months ago, asked a question with at least 3 up-votes. For DESeq2 proper design setting
Scholar 6 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Voter 6 months ago, voted more than 100 times.
Scholar 6 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Guru 6 months ago, received more than 100 upvotes.
Scholar 6 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 7 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 7 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 7 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 7 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: How to add tophat and bowtie to the path?
Scholar 8 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 8 months ago, created an answer that has been accepted. For A: How to convert .bed file to .juncs file using Tophat?

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