User: Wietje

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Wietje120
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Posts by Wietje

<prev • 32 results • page 1 of 4 • next >
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Comment: C: Read MAP and PED files in PLINK
... Could you provide an excerpt from the map file? And most importantly - in your directory screenshot the PED and MAP file are listed as text documents, so apparently something went wrong when saving the file. Did you export directly from Excel? I often exported to Notepad (text editor) first with cop ...
written 14 days ago by Wietje120
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Answer: A: Read MAP and PED files in PLINK
... Could you tell us what error message you got exactly and what your code was? That would help with debugging... ...
written 14 days ago by Wietje120
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Answer: A: How to create heatmaps only with DE genes in edgeR
... Have you tried to build a subset with those 20 genes? I assume you have one gene per row in which case you should take a look at this post: [https://www.biostars.org/p/186063/][1] [1]: https://www.biostars.org/p/186063/ From there on the process should be exactly the same. Does this help you? ...
written 14 days ago by Wietje120
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Answer: A: Sort the 'score' value for each aligned sequence
... Assuming your file is loaded as a dataframe, youcould give this a try (how exactly did you use order() on your data? could you provide the actual code you used?): x= df[order(df[,"score"],decreasing = TRUE), ] This should sort your dataframe in decreasing order based on the score (make sure "s ...
written 26 days ago by Wietje120
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Answer: A: Calculate the genotype frequency
... You might want to try PLINK which allows you to read in a VCF file (--vcf [INPUTFILE]), select only a few individuals (--keep [FILE]) and then get genotype frequencies with --freqx (with aditional option --nonfounders if you want to have it for all individuals in your list) or allele frequencis with ...
written 26 days ago by Wietje120
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Comment: C: FeatureCounts fails to count fragments instead of reads
... Not necessarily, there are also unpaired reads in the file, but the multialigning ones happen to be paired most of the time as far as I can see. ...
written 4 weeks ago by Wietje120
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Comment: C: FeatureCounts fails to count fragments instead of reads
... Yes, I only filtered for "listed first in the file", something like this: samtools view -h input.bam | awk -F"\t" '{if(NR>3319 && NR<3369 && $22!="NH:i:1" || NR>3319 && NR<3369 && $23!="NH:i:1"); else print $0}'|samtools view -bS - > new.bam The ...
written 4 weeks ago by Wietje120
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Comment: C: FeatureCounts fails to count fragments instead of reads
... Thank you for the link, that confirms part of my idea. I would however assume that featureCounts does only take the first X reads into account when concluding on SE or PE reads, right? ...
written 4 weeks ago by Wietje120
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FeatureCounts fails to count fragments instead of reads
... Hello fellow Biostars, I recently stumbled across the phenomenon that FeatureCounts fails to count fragments instead of reads, despite the command option -p. This only seems to happen when the input BAM file starts with several multialigning reads and contains the **tag NH:i:10**. The problem then ...
featurecounts fragment counting reads rna-seq written 4 weeks ago by Wietje120 • updated 4 weeks ago by JJ300
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Answer: A: How to extract genes 10000 bp upstream and 1000 bp downstream of long non coding
... Bedtools has the option "closest" which allows you to search for genes close to your specified locus. You can exclude directly overlapping (i.e. touching) genes and also ask for the distance to your locus and then sort by it for instance. I am not sure whether you can actually specify 1000bp distanc ...
written 9 weeks ago by Wietje120

Latest awards to Wietje

Scholar 14 days ago, created an answer that has been accepted. For C: Bedtools intersect QTL animalgenome
Scholar 3 months ago, created an answer that has been accepted. For C: Bedtools intersect QTL animalgenome
Scholar 10 months ago, created an answer that has been accepted. For C: Bedtools intersect QTL animalgenome

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