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JBerthelier / PiRATE

PiRATE (Pipeline to Retrieve and Annotate Transposable Elements)
http://doi.org/10.17882/51795
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Statistics summary #49

Closed pwkooij closed 4 years ago

pwkooij commented 4 years ago

Hi Jeremy,

Is it possible to generate a statistics summary similar to the table 1 in the paper? Or how can I easily extract the numbers of the different TE's and proportions of the genome etc?

Cheers Pepijn

JBerthelier commented 4 years ago

Dear Pepjin, The annotation is based on the tool TEannot which, unfortunately do not provide automatic statistic for the TE class / order or familly.

In my case, I have used the annotation (gff) file to calculate the percentage / content of each TE class (order or family). I have simply use a speardsheet such as excel.

Nb: some annotations can overlap, because sometime TE can insert into other ones, or due to technical artefacts. If you want to avoid overlap (because it gonna increase the real percentage of total TEs in the genome) you can use the tool named '' bedtool merge''. This tool will merge overlaping annotations.

Best,

Jeremy

pwkooij commented 4 years ago

Hi Jeremy

Thanks for the quick response. I noticed that the gff output is by contig, leading to a lot of separate files. Do you know an easy way to concatenate them into one file?

Cheers Pepijn

JBerthelier commented 4 years ago

Hi pepijn,You can use the Linux command "cat" from the Linux konsol to concatenate all files. You can use the command cat > output.gff(the means to concatenate all files that are in a same directory) Please check tuto on Google if you are not familiar with Linux command. Best Jeremy-------- Message original --------Objet : Re: [JBerthelier/PiRATE] Statistics summary (#49)De : pwkooij À : JBerthelier/PiRATE Cc : Jérémy Berthelier ,Comment Hi Jeremy Thanks for the quick response. I noticed that the gff output is by contig, leading to a lot of separate files. Do you know an easy way to concatenate them into one file? Cheers Pepijn

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