User: cschu181

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Posts by cschu181

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Answer: C: What is the minimum number/threshold of gaps (NNNNNN) permitted in a draft genom
... I'd say this is expected. Since you're only using short reads your contigs/scaffolds cannot bridge certain low complexity, repetitive regions, so the assembly process will introduce stretches of N where assembly paths cannot be uniquely resolved. I wouldn't worry about this. ...
written 16 days ago by cschu1811.7k
2
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Comment: C: STAR on Galaxy
... Memory is not storage. How much RAM do you have available in your instance? STAR is kinda known to need a lot of that. ...
written 6 weeks ago by cschu1811.7k
4
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Answer: C: Using awk or sed to edit a column in a gtf file
... awk -v OFS="\t" -v FS="\t" '{ $2=gensub("^mRNA.", "", 0, $2); print $0; }' your_file > your_modified_file Edit: removed tab-separated assumption, as I just saw it should treat a gtf, which we all know is tab-separated. ...
written 7 weeks ago by cschu1811.7k
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Comment: C: Trinity assembly file
... For the second question: awk '{ print $1; }' Trinity.fasta ...
written 9 weeks ago by cschu1811.7k
2
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Comment: C: Scientific Programmer DSM Biotechnology Center, Delft the Netherlands
... What does "local contract" mean? I assume that means non-remote/office-based? ...
written 9 weeks ago by cschu1811.7k
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Comment: C: Need help with my Needleman-Wunsch Python program (traceback) (error)
... It seems you're using the wrong scores: if x==0: f1=float("-inf") **f2=matrix[i-1][x]** f3=float("-inf") elif i==0: f1=float("-inf") f2=float("-inf") **f3=matrix[i][x-1]** ...
written 10 weeks ago by cschu1811.7k
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Comment: C: How to deal with gaps during translation with biopython
... Is there any reason that the gaps need to be translated? There is no gap in the actual sequence, so tt-aaaatg would have a frameshift in relation to tttaaaatg and code for LK instead of FKM. Just for the sake of it, you could try to see what the biopython translation engine does with "N" in nuclei ...
written 11 weeks ago by cschu1811.7k
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Comment: C: Prokka Annotation for Bacterial Transcriptomes
... Find the ORFs in your transcripts (e.g. with transdecoder) and then blastx (or translate and blastp) against a bacterial protein database. Transcripts without ORFs and those without hits you could process with RNA finding tools (tRNAscan, Infernal, SortmeRNA etc.) and blastn against ncRNA databases. ...
written 12 weeks ago by cschu1811.7k
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Comment: C: Folding RNA on python
... Have you looked at [RNAsketch][1]? This is a Python wrapper for the Vienna Package, which might give you just what you want. [1]: https://github.com/ViennaRNA/RNAsketch ...
written 3 months ago by cschu1811.7k
0
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Comment: C: Determining which strain trinity contig belongs to after denovoassembly
... Align the reads from your samples against the contig. Then you can either visually check the bam files in a browser (IGV etc.) or probe the position with some naive variant calling, e.g samtools mpileup. ...
written 3 months ago by cschu1811.7k

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