User: nterhoeven

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nterhoeven120
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Posts by nterhoeven

<prev • 33 results • page 1 of 4 • next >
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Comment: C: Low BUSCO completeness value for protists
... Does your organism have any special genomic features or occupies a small niche? Parasites, for example, often have a reduced gene set. The same goes for other highly specialised organisms. In that case, I would not worry too much about a low busco completeness, as I would expect differences from a " ...
written 9 months ago by nterhoeven120
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Answer: A: export picture from R studio
... You can export plots from **R** with this: pdf("filename.pdf") plot(myData1) plot(myData2) dev.off() This will create a pdf with two pages showing the two plots. Alternatively, you can use `png()`or `svg()`instead of `pdf()`, if you want a different file format. There are also lot ...
written 11 months ago by nterhoeven120 • updated 11 months ago by zx87549.6k
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Answer: A: Merge two columns...
... You can do this with `left_join()` from the `tidyverse` package You should rename the `log2FC` columns to different names and then run `left_join(tabelle1,tabelle2)`. This will merge the two data frames by the common column (`genID`). Take a look at https://stat545.com/join-cheatsheet.html for mor ...
written 12 months ago by nterhoeven120
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Answer: A: Awk or Shell script in need
... I would use the following `perl` one-liner for this: perl -ane 'BEGIN{$id="";} if($F[0] ne $id){$id=shift(@F); print $id,"\n",join(" ",@F),"\n";}else{shift(@F); print join(" ",@F),"\n";}' filename.txt Explanation: - The file is read line-wise and each line is split at whitespace - The first c ...
written 3.9 years ago by nterhoeven120
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Comment: C: Count repeat sequence
... Or shorter using perl ;-) perl -ne 'print $_=~y/ACT//' or if you want the percentage: perl -ne '$l=length($_);$m=$_=~y/ACT//; print $m/$l*100' ...
written 4.2 years ago by nterhoeven120
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Answer: A: How to concatenate gene sequence?
... This should work for you: cat * | perl -ne 'BEGIN{print ">concat\n"}next if $_=~/^>/; chomp; print $_;' > concat.fa This line concatenates all files in your directory and passes the output to perl. Then perl prints a header line (`>concat`) and every line (which does not start with ...
written 4.8 years ago by nterhoeven120 • updated 9 months ago by RamRS30k
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Comment: C: How to concatenate multiple blastx output file in a way that all the hits from o
... I am not very familiar with python. So, I cannot see from the code you posted, how the script reads the input. I would recommend to take a small test dataset (where you know the result) and try the command I posted before. Also, you should take a look at a manual, or ask the author of the script, h ...
written 4.8 years ago by nterhoeven120 • updated 9 months ago by RamRS30k
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Comment: C: How to concatenate multiple blastx output file in a way that all the hits from o
... You should use a scripting language, if you want to ge a more advanced sorting (like hits sorted by score for each query). The command I posted sort alphabetically. ...
written 4.8 years ago by nterhoeven120
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Comment: C: How to concatenate multiple blastx output file in a way that all the hits from o
... You could try something like cat file1 file2 | sort This would first concatenate your files and then sort the lines. This way, you get a "block" for each query. ...
written 4.8 years ago by nterhoeven120 • updated 9 months ago by RamRS30k
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Comment: C: Error while mapping reads to assembly using bowtie
... you seem to have a problem with your fastq file. You should take a look at it. Especially at the read named in the error message. Try: grep -C 4 'DHKW5DQ1:246:C1D7AACXX:4:1101' ...
written 4.9 years ago by nterhoeven120

Latest awards to nterhoeven

Teacher 11 months ago, created an answer with at least 3 up-votes. For A: export picture from R studio
Scholar 3.9 years ago, created an answer that has been accepted. For A: Awk or Shell script in need

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