User: michael.ante

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michael.ante1.9k
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Posts by michael.ante

<prev • 203 results • page 1 of 21 • next >
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Comment: C: 'std::ios_base::failure while running STAR
... According to your script, you run index generation and alignment simultaneously. This will not work. Please read the manual, compute the index first and run afterwards the alignment. ...
written 2 days ago by michael.ante1.9k
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Comment: C: high % of reads mapped to multiple loci after STAR mapping
... Was anything suspicious in the FastQC report? Have you checked for rRNA or other contamination? For RNA-Seq, I'd use the ENCODE settings described in the STAR manual. This parameter set worked well for me in various experiments. ...
written 6 days ago by michael.ante1.9k
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Answer: A: Extract Reads In Fastq Using A Bed File.
... I have a rather different approach in mind, but not fully tested. Using your BED file, you can extract the genomic sequences of interest as a fasta file (e.g. looping over the bed file and using samtools faidx). With BBSplit, you can extract all those fastq entries mapping to these regions. This sh ...
written 11 days ago by michael.ante1.9k
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Answer: A: htseq-count output file
... Hi Javad, you need to direct the output to a file : htseq-count -s no -t exon -i gene_id --additional-attr=gene_name Alignment-files annotation-files > result_file.txt Cheers, Michael ...
written 13 days ago by michael.ante1.9k
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Comment: C: Error while running STAR aligner
... After sorting out the memory issue, you should also add the parameter `--readFilesCommand zcat` , since your fastq files are zipped. ...
written 13 days ago by michael.ante1.9k
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Comment: C: Finding a variant's flanking sequence
... Check if you chromosomes' name start with 'chr' : head hg19.fa ...
written 14 days ago by michael.ante1.9k
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Comment: C: trimming PE RNA Reads
... I was mentioning the trimming in regard to the aligner. For de-novo assembly, I would remove the primer-sequences since they have a higher chance of incorporated mismatches. I don't know how trinity can cope with that. ...
written 15 days ago by michael.ante1.9k
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Comment: C: Tximport mixing annotations
... Hi Tania, have you tried this command on an unzipped GFF ? Cheers, Michael ...
written 19 days ago by michael.ante1.9k
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Comment: C: how to get ko definition by using KEGG API?
... Did you subscribe and pay the licence fee? If yes, you can contact the API's help desk. According to the manual at [kegg.net][1] the URL should look like this [http://www.kegg.jp/entry/K00873][2] . [1]: http://kegg.net [2]: http://www.kegg.jp/entry/K00873 ...
written 21 days ago by michael.ante1.9k
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Comment: C: Speed up Tophat2 running
... ... or the whole weekend. ...
written 23 days ago by michael.ante1.9k

Latest awards to michael.ante

Scholar 13 days ago, created an answer that has been accepted. For A: questions on rna-seq data analysis
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Commentator 10 weeks ago, created a comment with at least 3 up-votes. For C: Merge 2 files based on rs number but keep all info only from the first file
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