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isocircPlot - bedtools error unrecognized -nameOnly #14
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Please try to update your bedtools to least version, this should be fixed. |
Thanks. I am not sure if it has to do with bedtools or not...
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My feeling is that your input may be wrong. |
Ok that is true. I fixed that issue but I still get a similar error message. At the moment I just have 2 in the list file because I am just trying to get it to work before I go and add more. Is that a problem? I have the isocirc number or name and all the read ID's for both of them and the gene name.
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I have no idea. |
Sorry I got a bit busy with another project. I tried to run the test data and got this so I am not sure how to proceed. I have gotten it to work with my data so this error was a bit strange for me. isocirc -t 1 read_toy.fa chr16_toy.fa chr16_toy.gtf chr16_circRNA_toy.bed output Also, the isocirc.out file is missing but I guess I am supposed to generate that myself. |
Can you type 'cat read_toy.fa' and see what the fasta file contains? |
Sorry I was at a conference the past week. `cat read_toy.fa
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Looks like the fasta file has been modified, the ">" letters are missing. |
Hi,
I am trying to run the isocircPlot script and am getting an error with bedtools and I am not really sure what to do in this situation. Do you think it has to do with the version of bedtools or if there is something wrong with my input data?
Thanks.
Tool: bedtools getfasta (aka fastaFromBed)
Version: v2.27.1
Summary: Extract DNA sequences from a fasta file based on feature coordinates.
Usage: bedtools getfasta [OPTIONS] -fi -bed <bed/gff/vcf>
Options:
-fi Input FASTA file
-fo Output file (opt., default is STDOUT
-bed BED/GFF/VCF file of ranges to extract from -fi
-name Use the name field for the FASTA header
-name+ Use the name field and coordinates for the FASTA header
-split given BED12 fmt., extract and concatenate the sequences
from the BED "blocks" (e.g., exons)
-tab Write output in TAB delimited format.
- Default is FASTA format.
== date == [circRNA reference sequence] Error: bedtools getfasta -split -nameOnly -fi /X.fa -bed /isocirc.list -fo /circRNA_ref.fa
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