perl call_seq_by_list.pl is not working #118
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Please share a sample of your d file. Thanks.
Shujun
…On Wed, Apr 6, 2022 at 6:14 AM Ravindra Raut ***@***.***> wrote:
Hello Sir
I am getting empty output file after using *call_seq_by_list.pl
<http://call_seq_by_list.pl>*
I used gt suffixerator, gt ltrharvest, ltr_finder, LTR_retriever and awk
'{if ($1~/[0-9]+/) print $10"\t"$1}' to get the output_d file.
perl LTR_retriever/bin/call_seq_by_list.pl O_sativa_Hitomebore_output_d
-C O_sativa_Hitomebore.fa > O_sativa_Hitomebore_output_e
Please give some suggestion.
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Copia DG000053.1:155936..163480 |
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Above is the output_d file |
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I am using protocol by https://github.com/clavia96/LTR_retrotransposon/blob/main/Codes |
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Thanks for sharing the file. It looks correctly formatted. you may want to check your genome sequence IDs and see if they match. Thanks, |
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Hello, buddy! |
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Thank you very much @wensulin93. It worked !!!!! |
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I am not sure how the problem is solved, but I am glad that it works for you. The following file has inputs and outputs: test.zip Let me know if it does not work for you. |
Hello Sir
I am getting empty output file after using call_seq_by_list.pl
I used gt suffixerator, gt ltrharvest, ltr_finder, LTR_retriever and awk '{if ($1~/[0-9]+/) print $10"\t"$1}' to get the output_d file.
perl LTR_retriever/bin/call_seq_by_list.pl O_sativa_Hitomebore_output_d -C O_sativa_Hitomebore.fa > O_sativa_Hitomebore_output_e
Please give some suggestion.
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