User: michael.ante
michael.ante • 2.6k
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Posts by michael.ante
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... And if you have only CDS features, you want to set `-t CDS`. Otherwise htseq-count is only looking for exon features. ...
written 6 days ago by
michael.ante • 2.6k
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1
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... Did you try the option `-attrsOut=file` with gff3ToGenePred?
There you get
> output attributes of mRNA record to file. These are per-genePred row,
> not per-GFF3 record. Thery are derived from GFF3 attributes, not the
> attributes themselves. ...
written 7 days ago by
michael.ante • 2.6k
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... Hi caggtaagtat,
I'd check the gene expression with htseq-count or featureCounts setting the right stranded parameter for your library prep.
In human for instance, more than 75% of the mt-genes are located on the + strand. Having little expression on the minus-strand genes would explain your result ...
written 8 days ago by
michael.ante • 2.6k
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... Hi
You may have a look at this [answer][1]. The join command gives you quite nice output handling.
join -t $'\t' -1 3 -2 3 -a 1 -e "-" -o 1.1,1.2,0,1.4,1.5,1.6,1.7,1.8,1.9,1.10,2.13,2.14,2.15,2.16 file1.tsv file2.tsv
The `-1 3 -2 3` define the fields on which too join, the `-a 1` defines ...
written 13 days ago by
michael.ante • 2.6k
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... To learn python for bioinformatics, I'd recommend using [Rosalind][1].
It explains problems, how to solve these, and provides exemplary data.
[1]: http://rosalind.info/problems/locations/ ...
written 13 days ago by
michael.ante • 2.6k
0
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113
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... Hi k.kathirvel93,
Next to trausch's suggestion that bbmap's cigar string is per default in sam 1.4 notation (which can be switched by setting `sam=1.3`), BBmap uses the full fasta header for the chromosome name. Instead of having just e.g. "21" in the sam file, you have "21 dna:chromosome chromosom ...
written 14 days ago by
michael.ante • 2.6k
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105
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... I would not recommend adding rRNA sequences to your normal reference. These sequences are already in the mm10 reference as h.mon posted.
You could search e.g. NCBI nucleotide for the rRNA sequences in mouse and build a Bowtie index from these and map your data in a first step against it. Setting B ...
written 15 days ago by
michael.ante • 2.6k
1
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1
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134
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... BBmap is also capable of low-memory usage while index generation and mapping.
...
written 4 weeks ago by
michael.ante • 2.6k
1
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1
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96
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... Usually you count on the exon feature level, which is grouped on gene level. The gene feature which you are specifying with `-t gene` is not a standard feature (see [here][1]) and may be not included in your file.
Nevertheless, you'll get a table with the read count per gene if you leave the -t par ...
written 5 weeks ago by
michael.ante • 2.6k
1
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1
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104
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... Try the undocumented -Q33 option. The fastx toolkit is quite old and uses per default the phred 64 encoding. FastQ files are now encoded in phred 33.
Cheers,
Michael ...
written 5 weeks ago by
michael.ante • 2.6k
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