User: Macspider

gravatar for Macspider
Macspider2.4k
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Vienna - BOKU
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Posts by Macspider

<prev • 506 results • page 1 of 51 • next >
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Comment: C: R programming question
... It's not very clear how your data structure is: could you use appropriate brackets to separate them? Also, your question is very vague and I can't grasp what you want to do. Finally, when you post in Biostars as well as any other somehow-IT related forum, always copy-paste the error that you retr ...
written 12 days ago by Macspider2.4k
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Comment: C: Interpretation of Trimmomatic Results after Paired-End Adapter Trimming
... There is also the TruSeq2 file, and I usually have to use that one (i.e. most of the data files I trimmed were prepared with a TruSeq2 kit). ...
written 15 days ago by Macspider2.4k
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Comment: C: CDS sequence from mRNA and protein sequence
... I am interested in *which* software would be the way to go! ...
written 15 days ago by Macspider2.4k
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Comment: C: CDS sequence from mRNA and protein sequence
... Yes they are intronless! ...
written 15 days ago by Macspider2.4k
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CDS sequence from mRNA and protein sequence
... Hello guys, Here's for the (probably) dumb question of the day, but I can't seem to find fitting solutions in a reasonable amount of time, so I might be missing something here. I have an mRNA multifasta and a protein multifasta (IDs are correspondent between the two). What I'm after, is to get t ...
fasta cds protein code mrna written 15 days ago by Macspider2.4k • updated 15 days ago by lieven.sterck1.9k
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Comment: C: Interpretation of Trimmomatic Results after Paired-End Adapter Trimming
... Honestly, I don't have a clear answer to you on this matter, that's why I post it as a comment and not as an answer. I have some speculations though (maybe they help): - as far as I know it is easier to have adapter traces in the reverse reads with truseq kits, so it is probably easier to get for ...
written 15 days ago by Macspider2.4k
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Comment: C: Get the GO terms associated to all genes contained in a list with Python
... Well, it strongly depends on the oganism you work with! 99.9% you don't have such luck that someone already annotated all of them. Perhaps you should try something like Blast2GO where you input sequences and you get GOTerms out. ...
written 7 weeks ago by Macspider2.4k
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Comment: C: Get the GO terms associated to all genes contained in a list with Python
... I know it's not python, but you can definitely do that in R (I am also a python programmer but I went for R in that particular aspect). Have a look at GO.db: https://bioconductor.org/packages/release/data/annotation/html/GO.db.html ...
written 8 weeks ago by Macspider2.4k
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Read position bias (RPB and PV4) fields from samtools mpileup: how to get them?
... Hi all, How does anyone get the RPB and the PV4 into their VCF file? I can't ask for them in `mpileup -t ` and I can't ask for them anywhere else (or so I think). Here are the supported samtools mpileup tags at the moment: http://www.htslib.org/doc/samtools-1.0.html#mpileup Can someone help me? ...
rpb variant mpileup snp call written 8 weeks ago by Macspider2.4k • updated 8 weeks ago by al.bodrug50
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Comment: C: Which HTSeq mode is suitable for RNAseq data to be used for differential gene ex
... There is no "more suitable" one, all of them will do depending on what you want to achieve! I usually use union but you should check, biologically speaking, which one fits more your system. ...
written 8 weeks ago by Macspider2.4k

Latest awards to Macspider

Popular Question 7 weeks ago, created a question with more than 1,000 views. For Remove duplicates from reads: best practices?
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 4 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Appreciated 5 months ago, created a post with more than 5 votes. For Best way to compare two samples in a VCF file
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 5 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 6 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 6 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'
Scholar 7 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Popular Question 8 months ago, created a question with more than 1,000 views. For Remove duplicates from reads: best practices?
Appreciated 8 months ago, created a post with more than 5 votes. For Best way to compare two samples in a VCF file
Scholar 10 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to convert .bed file to .juncs file using Tophat?
Scholar 10 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Popular Question 11 months ago, created a question with more than 1,000 views. For Best way to compare two samples in a VCF file
Student 14 months ago, asked a question with at least 3 up-votes. For DESeq2 proper design setting
Scholar 14 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
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Scholar 14 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
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Scholar 14 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'

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