an issue by using using FEELnc_filter.pl

[yxlong032]

Recently, I tried to analyse the lncRNA profile of porcine tissues by using FEELnc.

Requirements were already installed as the descriptions on "https://github.com/tderrien/FEELnc".

However, while using FEELnc_filter.pl, some error information occurred at my Computer Terminal, looked like this: "Child 13 encountered an unknown erroe at FEELnc_filter.pl line 159"

Can somebody give me advice to resolve this issue?

[Tichaboni]

Hello, Testing FEELnc with the following ~/FEELnc/test$ FEELnc_filter.pl -i transcript_chr38.gtf -a annotation_chr38.gtf \ gave me the error FEELnc_filter.pl: command not found Would you please help me resolve this. I get the same error (command not found) with FEELnc_codpot.pl -i candidate_lncRNA.gtf -a annotation_chr38.gtf -b transcript_biotype=protein_coding -g genome_chr38.fa --mode=shuffle and FEELnc_classifier.pl -i feelnc_codpot_out/candidate_lncRNA.gtf.lncRNA.gtf -a annotation_chr38.gtf > candidate_lncRNA_classes.txt

Your help will be highly appreciated

[Tichaboni]

Hello, I was able to add FEELnc to the computer variables and run the toy examples. My input files are in FASTA format. When I run this command on terminal

FEELnc_filter.pl -i FLchicken.fa -a Gallus_gallusannotation.gtf \ -b transcript_biotype=protein_coding > FLchicken1candidate

I get the error

Error: Cannot read your input GTF file 'FLchicken.fasta'...

What do I need to change? The write-up says the input file can be in GTF or FASTA format.

On Mon, Oct 30, 2017 at 1:23 AM, yxlong032 notifications@github.com wrote:

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Hi, This raised issue may be due that FEELnc hasn't been added into your computer variables, like the description at github:I hope it will help you.

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On 10/28/2017 00:48，Tichaboninotifications@github.com wrote：

Hello, Testing FEELnc with the following ~/FEELnc/test$ FEELnc_filter.pl -i transcript_chr38.gtf -a annotation_chr38.gtf \ gave me the error FEELnc_filter.pl: command not found Would you please help me resolve this. I get the same error (command not found) with FEELnc_codpot.pl -i candidate_lncRNA.gtf -a annotation_chr38.gtf -b transcript_biotype=protein_coding -g genome_chr38.fa --mode=shuffle and FEELnc_classifier.pl -i feelnc_codpot_out/candidate_lncRNA.gtf.lncRNA.gtf -a annotation_chr38.gtf > candidate_lncRNA_classes.txt Your help will be highly appreciated

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— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/tderrien/FEELnc/issues/16#issuecomment-340353946, or mute the thread https://github.com/notifications/unsubscribe-auth/AdqteaR6Mb-WL1Jp8PunKOLwfj7MFq-hks5sxWtmgaJpZM4QAWQ5 .

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[vwucher]

Hi,

Sorry for the big delay...

@Tichaboni: as yxlong032 said, the filter module can only be used with a GTF. Because it check is the annotation (GTF) of your input file is overlapping the reference annotation. For FASTA files, only the coding potential module is available.

@yxlong032: I think this error rise because of an issue on the child process, i.e. when the filtering is split between several processor. Can you check running the filter using only one processor using this option: --proc=1

Thanks, Valentin Wucher

[yxlong032]

Hi, Valentin Wucher, I run the filter module by using only one Processor, but the similar error occured agian:

"Child AEMK02000439.1 encountered an unknown error at /public/home/yxl/yuanxiaolong/lncRNA/software/FEELnc/scripts/FEELnc_filter.pl line 159."

Then How should I do ?

[tderrien]

Hello yxlong032,

This error is probably related to the Parallel::ForkManager library which allows FEELnc to parallelise the process of filtering candidate lncRNAs. As it is the first time I see this error, I just have 2 suggestions/questions:

• Which versions of Parallel::ForkManager and Perl are installed on your OS? As noted in the README, version 1.07 of P::FM and Perl 5.18.2 were tested.
• If the same versions were used, I'd suggest to try an alternative such as bedtools to remove assembled transcripts that overlap protein_coding transcripts.

Let me know if this helps

Best,

Thomas

[Tichaboni]

Hi I have used FEELnc to identify lncRNA in RNA-seq data. I would like to compare the expression of these lncRNAs in two sets of samples as well as show which lncRNAs are shared between the groups. Would you recommend a method to do this? Kimathi.