User: michael.ante

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michael.ante2.5k
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Posts by michael.ante

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Comment: C: cufflink output FPKM values
... Hi, There is a difference between Cufflinks mentioned gff (should be gff2) and a gff3 file. Since you named your file.gff3, i was suggesting to use rather gtf. In your GFF file, there is no aggregation on gene level. Thus, Cufflinks cannot make a connection between an isoform and a gene. You may ...
written 8 days ago by michael.ante2.5k
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Comment: C: Using multiple gff files for featureCounts tool
... Why not pasting all gff into a single file? cat *gff > my_annotation.gff ...
written 10 days ago by michael.ante2.5k
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Answer: A: cufflink output FPKM values
... Hi blooming.daisy333, First, people will tell you not to use Cufflinks any more but StringTie. You might here their point. AFAIK, Cufflinks needs a GTF file but you are supplying a GFF3 file. Could you get the annotation also in GTF format? If not, you may try to convert it with the [UCSC tools][1 ...
written 10 days ago by michael.ante2.5k
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Comment: C: More efficient way than zipping arrays for transposing a FinalReport table in Py
... Have you tried CSVTK's transpose ([here][1])? The tools is working well on my tables, but these aren't that big. [1]: http://bioinf.shenwei.me/csvtk/usage/#transpose ...
written 21 days ago by michael.ante2.5k
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Comment: C: High Unassigned Ambiguity in Feature Counts
... Hi DVA, You're right featurecounts' starndedness parameter is not mentioned in the listed parameter on the CL. According to the [webpage][1] : > Perform strand-specific read counting (use '-s 2' if reversely stranded): > > featureCounts -s 1 -t exon -g gene_id -a annotation.gtf -o counts ...
written 23 days ago by michael.ante2.5k
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Answer: A: High Unassigned Ambiguity in Feature Counts
... Hi DVA, In many genomes, you have overlapping genes on different strands. Without correct orientation, the reads will not be assigned without ambiguity. Is your 3' seq protocol strand specific? If so, you should run featureCount with the corresponding parameter. You can run e.g. [infer_experimen ...
written 25 days ago by michael.ante2.5k
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Answer: A: match gives me all NA in annotating my genes
... Hi, in your annot table, the column transcript_cluster_id consists of numerical values. There should not be any match. In this case the match function return the value, given by the parameter 'nomatch'. I guess, you can try match on the gene assignment. As fara as I remember, there are also a lot ...
written 10 weeks ago by michael.ante2.5k
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Comment: C: samtools - Finding Average Fragment size for pair?
... I'm not familiar with exome sequencing. Did you have splices in your aligned reads, or is the whole gene including introns covered? With splicings have a look at [RSeQC][1]; without splicings have a look at [bedtools][2] [1]: http://rseqc.sourceforge.net/ [2]: http://bedtools.readthedocs.io/e ...
written 10 weeks ago by michael.ante2.5k
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Answer: C: HISAT output SAM file incorrect (only contains 3 columns of data)
... I think Sej is pointing in the right direction: you are seeing the sam file's header; which can be quite long. You can use `samtools view -S 21divv1.sam` to see only the reads. ...
written 10 weeks ago by michael.ante2.5k
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Answer: A: samtools - Finding Average Fragment size for pair?
... Do you have RNA-Seq or DNA-Seq data? With DNA, you may just use bedtool's bamtobed with the bedpe option and compute the length. For RNA-Seq you can have a look at RSEQC's inner_distance.py. Which you could adapt to your needs. Cheers, Michael ...
written 10 weeks ago by michael.ante2.5k

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