User: Macspider

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

<prev • 495 results • page 1 of 50 • next >
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Variant distance bias (VDB) in VCF format: how to compute properly?
... Hi guys, Does anyone of you have experience with computing the variant distance bias (VDB) value for VCF-formatted files? I am trying to figure out myself how to do it, but literature / documentation / discussion on it is quite scarce. So far, what I know is: - The higher the value, the bigg ...
vcf vdb variant distance bias written 6 days ago by Macspider2.4k
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Comment: C: i have an overlap between my reference and non-reference sample !
... Impute with which tool? What is your reference file format? What are MSL individuals? ...
written 7 days ago by Macspider2.4k
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Converting blastn output to VCF (for SNPs): what is the quickest way?
... Hello guys, Title is pretty self-explanatory: what is the quickest way to convert the output of command line blast (say xml format, but I'm open to any suggestion) to a pseudo-VCF file? I am interested in getting all the positions where I have a SNP (mismatch) between query and subject. Doesn't ...
vcf xml blast snp convert written 19 days ago by Macspider2.4k
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Comment: C: building index with HISAT2
... Each reference has to have its own index. You are currently loading many references (i.e. all the fasta files you have as comma-separated) and sending them to one only reference basename (hisat_index). If you have, say, three reference sequences named 1.fa, 2.fa and 3.fa, your command should have ...
written 27 days ago by Macspider2.4k
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Comment: C: Phred 33 and phred 64 scores mixed in .bam file
... I am having the same problem in this moment, did you manage to solve it? If yes, how? ...
written 28 days ago by Macspider2.4k
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Answer: A: building index with HISAT2
... You're specifying the path only for the first file: `/data/memona/reference/` Move into that directory and then run hisat2 without the path specification. Also, as fair as I know, you have to specify as many index basenames as there are input files, the same way (comma separated). ...
written 28 days ago by Macspider2.4k
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Comment: C: Java Exception in Running Trimmomatic software
... Check if you have an empty line at the beginning / end of the file. ...
written 4 weeks ago by Macspider2.4k
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Answer: A: strange htseq-count result
... > -s no This is (imho) the problem. Perhaps your library is stranded. I'm saying this because I see ~ half of the scores in __no_feature and another half in __ambiguous. Try `-s yes`! ...
written 4 weeks ago by Macspider2.4k
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Comment: C: SNP/Mbp rate weird, any known bias/artifact?
... Actually, it is not exactly as you said: > one contains calls on the whole genome, the other contains an subset of it I don't have a non-CDS group and a CDS group, I have a whole-genome (including CDS) and a CDS only. Also, I am quite confident on the annotation because it was done by me, so ...
written 4 weeks ago by Macspider2.4k
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SNP/Mbp rate weird, any known bias/artifact?
... Hello guys, I am working with rates of variation (expressed in SNP/Mbp) and I'm observing something which biologically doesn't have much sense. I have two variant call sets: one contains calls on the whole genome, the other contains an subset of it, made on the coding regions only (CDS lines in GF ...
mbp calling variant snp bias written 4 weeks ago by Macspider2.4k

Latest awards to Macspider

Teacher 27 days ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 12 weeks ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Appreciated 3 months ago, created a post with more than 5 votes. For Best way to compare two samples in a VCF file
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 3 months ago, created an answer that has been accepted. 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'
Scholar 4 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
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 5 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Popular Question 6 months ago, created a question with more than 1,000 views. For Remove duplicates from reads: best practices?
Appreciated 6 months ago, created a post with more than 5 votes. For Best way to compare two samples in a VCF file
Scholar 8 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'
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How to convert .bed file to .juncs file using Tophat?
Scholar 8 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Popular Question 9 months ago, created a question with more than 1,000 views. For Best way to compare two samples in a VCF file
Student 12 months ago, asked a question with at least 3 up-votes. For DESeq2 proper design setting
Scholar 12 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 12 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 12 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
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Teacher 13 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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