User: mxlsherry1992

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Posts by mxlsherry1992

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Comment: C: intersection for several file
... It worked! Thank you ...
written 1 day ago by mxlsherry199210
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intersection for several file
... Dear all, If I have 6 files, each file only has one column (gene ID), I want to extracted the intersection for those 6 files, which command should I use? I know the below command can work for 2 files, but not for 6 files: cat file1 file2 | sort | uniq -d > intersection.out Thanks and ha ...
script rna-seq sequencing written 2 days ago by mxlsherry199210 • updated 2 days ago by manuel.belmadani800
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Orthogroups.csv file for orthofinder
... Dear all, To interpret the orthofinder output file Orthogroups.csv, if I have three input protein fasta file, the output Orthogroups.csv is like below, the first two species have no reference genome, so its' ID looks like"Trinity_DN_...", since the ID has similar format for the first two species( ...
assembly alignment rna-seq sequencing written 5 days ago by mxlsherry199210 • updated 3 days ago by SMK320
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Comment: C: Trinity assembly file
... It worked !! Thank you!! ...
written 5 days ago by mxlsherry199210
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Trinity assembly file
... Dear all, I meet two problems when deal with the Trinity assembled fasta file... After trinity assembly, I got an fasta file, but in order to get the unigene, do I need to use "cd-hit" or "get_longest_isoform_seq_per_trinity_gene.pl" to deal with this fasta file? I am not sure which one should I u ...
assembly rna-seq sequencing written 6 days ago by mxlsherry199210
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Comment: C: orthofinder software results
... Thanks for your kindly reply!! I think I made a mistake for the input file of Orthofinder then results in too much sequence in output file. for the data without reference genome, I just use cd-hit and transdecoder to get the protein file, do I need to use "get_longest_isoform_seq_per_trinity_gene.pl ...
written 6 days ago by mxlsherry199210
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orthofinder software results
... Dear all, I got some confused when analyzing the Orthofinder results. I have three RNA-sequencing data for A, B,C species (A has refenrence genome and B,C haven't have a reference genome), My aim is to find the genes existed in B, C species, but absent in A species. I think Orthofinder should be w ...
assembly next-gen rna-seq written 8 days ago by mxlsherry199210 • updated 8 days ago by lieven.sterck4.8k
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Comment: C: NCBI nucleotide ID to protein ID
... Thank you! I solved this problems! it worked finally!! ...
written 9 days ago by mxlsherry199210
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Comment: C: NCBI nucleotide ID to protein ID
... Hi, I downloaded the Channel Catfish gff file from NCBI, however, there is nucleotide ID colume like "XM_017496642.1", and NCBI ID colume like "108281084", but there is not a colume contain protein ID for me to link...I also didn't find a file containing both nucleotide ID and protein ID for me to ...
written 12 days ago by mxlsherry199210
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Comment: C: NCBI nucleotide ID to protein ID
... Hi, Thanks for your patience.. I tried to submit the script to the background with "qsub -F script.sh idfile.txt" and it reports a similar error line 9: nucl_id: No such file or directory line 10: protein_out: No such file or directory sed: can't read protein_out_mod: No such file o ...
written 12 days ago by mxlsherry199210

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