User: David Fredman

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David Fredman990
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University of Bergen, Norway
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http://www.davidfredma...
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davfre
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2 years ago
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6 years, 11 months ago
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Computational biologist, programmer & data analyst. I study genome/transcriptome/regulatory function and evolution

Posts by David Fredman

<prev • 49 results • page 1 of 5 • next >
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Answer: A: how to get actual gene sequence after cufflinks
... Use the gffread tool that comes bundled with cufflinks gffread -g genome_reference.fasta -w transcript_sequences.fasta assembled_transcripts.gtf ...
written 4.4 years ago by David Fredman990
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Comment: C: Counting sense reads in bacterial paired-end RNA-seq data
... Try bedtools intersect (full documentation of options at https://bedtools.readthedocs.org/en/latest/content/tools/intersect.html) Your command might look something like this (not tested): bedtools intersect -S -c -a genes.bed -b mapped_reads.bam That will output the count of reads overlapping on ...
written 4.4 years ago by David Fredman990
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Answer: A: rnahybrid "Error in nextSQ. Aborting"
... A guess on the error message - your fasta file ends with an empty line or similar, that makes the Fasta parser in RNAhybrid fail on trying to parse it. Alternatively, you have a malformatted fasta entry in a multi-fasta sequence. Do you get results for all your UTR and miRNA sequences, or does it st ...
written 4.5 years ago by David Fredman990
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Answer: A: R Equivalent of Cross-Gene Error Model (CGEM) (Rocke and Durbin 2001).
... The background correction and mean-variance estimation in the vsn package http://www.bioconductor.org/packages/release/bioc/html/vsn.html or the RMA method in the affy package might do what you need?   ...
written 4.5 years ago by David Fredman990
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Comment: C: Rank Genes By FPKM for only One Sample
... No further normalization is required to compare the expression of genes within one sample. Just sort (rank) your genes by their FPKM or TPM values. You can do this in Excel (!), the *nix command line, or any programming language (including R). Those with the highest values are most abundant transcri ...
written 4.5 years ago by David Fredman990
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Comment: C: gft to fasta conversion
... that's odd. assuming that the chromosome names were correct, then the only reason I could think of would be a gff format that gffread does not understand..  Either try to validate your gff, or try a different tool. Perhaps bedtools will be more forgiving http://bedtools.readthedocs.org/en/latest/c ...
written 4.5 years ago by David Fredman990
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Comment: C: gft to fasta conversion
... gffread your_transcripts.gff -g genomic_reference.fasta -w your_transcripts.fasta​   Make sure that the chromosome/scaffold ids are the same in gff and genomic reference (capitals, underscores etc). ...
written 4.5 years ago by David Fredman990
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Answer: A: gft to fasta conversion
... The gffread utility in the Cufflinks package will extract transcript fasta given a gtf/gff and reference (genome) fasta file. For all the options: gffread -h To get only the DE transcripts, either subset the gff/gtf or, perhaps more straightforward, subset the fasta file (see here for multiple wa ...
written 4.5 years ago by David Fredman990
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Job: (Closed) Researcher in informatics - Genomics and Computational Biology, Bergen, Norway
... The University of Bergen (UiB) is an internationally recognised research university with more than 14,000 students and close to 3,500 employees at six faculties. The university is located in the heart of Bergen. Our main contribution to society is excellent basic research and education ...
next-gen job rna-seq sequencing written 4.5 years ago by David Fredman990
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Comment: C: Looking for a tool to do GO enrichment analysis with BLAST2GO output(s)
... Dear Anki,   Do I understand it correctly that your complete gene set consists of 650 transcripts, of which 130 are annotated with a GO term? Is that the complete transcriptome, or are these genes that you found to be differentially expressed? In the example provided in the vignette you are refer ...
written 4.5 years ago by David Fredman990

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Appreciated 3.1 years ago, created a post with more than 5 votes. For A: Best tools for circular genome visualization?
Good Answer 3.1 years ago, created an answer that was upvoted at least 5 times. For A: Best tools for circular genome visualization?
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: How to sort PDB name
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: How to sort PDB name
Good Answer 4.1 years ago, created an answer that was upvoted at least 5 times. For A: Best tools for circular genome visualization?
Appreciated 4.2 years ago, created a post with more than 5 votes. For A: Best tools for circular genome visualization?
Teacher 4.4 years ago, created an answer with at least 3 up-votes. For A: How to sort PDB name
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Good Answer 4.9 years ago, created an answer that was upvoted at least 5 times. For A: Best tools for circular genome visualization?
Appreciated 4.9 years ago, created a post with more than 5 votes. For A: Best tools for circular genome visualization?
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: How to sort PDB name
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Scholar 4.9 years ago, created an answer that has been accepted. For A: How to sort PDB name
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: How to sort PDB name
Appreciated 4.9 years ago, created a post with more than 5 votes. For A: Best tools for circular genome visualization?
Good Answer 4.9 years ago, created an answer that was upvoted at least 5 times. For A: Best tools for circular genome visualization?
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: How to sort PDB name
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Scholar 4.9 years ago, created an answer that has been accepted. For A: TCGA: What are mRNA expression z-scores? Does TCGA have mRNA expression from con
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Scholar 4.9 years ago, created an answer that has been accepted. For A: TCGA: What are mRNA expression z-scores? Does TCGA have mRNA expression from con
Scholar 4.9 years ago, created an answer that has been accepted. For A: TCGA: What are mRNA expression z-scores? Does TCGA have mRNA expression from con
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: TCGA: What are mRNA expression z-scores? Does TCGA have mRNA expression from con

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