Question

how to extract the longest isoform from trinity outfils

2

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7.1 years ago

wu.zhiqiang.1020 ▴ 50

Dear all,

I want to filtered the Trinity outfile for RNAseq assemble. I know this is not the best choice, and there are some scripts online. but they are all not good to use in my data, Could you give me some suggestion on this?

my data like this: (Start with > for name)

TRINITY_DN66086_c0_g1_i1 len=1158 path=[1258:0-49 1259:50-66 1268:67-201 1262:202-225 1267:226-656 1257:657-1157] [-1, 1258, 1259, 1268, 1262, 1267, 1257, -2] CTAGCCTACGGGGCTTTATTGGGTCACTTTTTCCAATCGAGTTTGCGGAAAGGCCTCTTT CGGCGGAGCCCTTACGCCTCGTGAAACGAGATATTCAGGGCTCCCCGAAAGGGCACGGCT

TRINITY_DN66086_c0_g1_i2 len=1207 path=[1253:0-49 1254:50-115 1268:116-250 1262:251-274 1267:275-705 1257:706-1206] [-1, 1253, 1254, 1268, 1262, 1267, 1257, -2] CTAGCCTACGGGGCTTTATTGGGTCACTTTTTCCAATCGAGTTTGCGGAAGAGGCTTTTC CACCATTTGGCCCAGTCTAGCCGGGGCCACATGGCGGAAAGGCCTCTTTCGGCGGAGCCC TTACGCCTCGTGAAACGAGATATTCAGGGCTCCCCGAAAGGGCACGGCTGCTCTTCCTTG G

How can I get the longest one for the same gene cluster?

thanks

Assembly RNA-Seq • 6.0k views

ADD COMMENT • link updated 4.8 years ago by Shahzad ▴ 30 • written 7.1 years ago by wu.zhiqiang.1020 ▴ 50

0

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Dear All

I am using "get_longest_isoform_seq_per_trinity_gene.pl" script

Please help to solve this error. I also have installed the perl module Bio::Index::Fasta but the error is still there.

Can't locate Fasta_reader.pm in @INC (you may need to install the Fasta_reader module) (@INC contains: /home/ubuntu/Desktop/isoform/../../PerlLib /home/ubuntu/perl5/lib/perl5 /home/ubuntu/miniconda3/envs/longiso/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/ubuntu/miniconda3/envs/longiso/lib/site_perl/5.26.2 /home/ubuntu/miniconda3/envs/longiso/lib/5.26.2/x86_64-linux-thread-multi /home/ubuntu/miniconda3/envs/longiso/lib/5.26.2 .) at get_longest_isoform_seq_per_trinity_gene.pl line 7.
BEGIN failed--compilation aborted at get_longest_isoform_seq_per_trinity_gene.pl line 7.

ADD REPLY • link updated 4.8 years ago by GenoMax 141k • written 4.8 years ago by Shahzad ▴ 30

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Looks like your $PERL5LIB variable is not correctly set. Something like: export PERL5LIB=/path_to/trinity/:${PERL5LIB} would be needed.

ADD REPLY • link 4.8 years ago by GenoMax 141k

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Or use conda to install the trinity, as it takes full care of dependencies and paths.

https://anaconda.org/bioconda/trinity

ADD REPLY • link 4.8 years ago by ATpoint 81k

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I have trinity installed by conda and trinity is working correctly for assembly

ADD REPLY • link 4.8 years ago by Shahzad ▴ 30

score 2 · Answer 1 · 2017-03-22

2

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7.1 years ago

h.mon 35k

$TRINITY_HOME/util/misc/get_longest_isoform_seq_per_trinity_gene.pl

ADD COMMENT • link 7.1 years ago by h.mon 35k

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It need other pm file to load and the same time. I find this link. But I have to search other more pm files also thanks

ADD REPLY • link 7.1 years ago by wu.zhiqiang.1020 ▴ 50

0

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If you install Trinity correctly and set $TRINITY_HOME, the script should work. Also, when reporting an error, please explain it in more detail - for example, copy the error message.