User: m.s_tabatabaei
m.s_tabatabaei • 0
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Posts by m.s_tabatabaei
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... Hi every one,
I run the Blastx aginst nr using this commend line "
blastx -db blastdb_Nr/Blast_Nr -query Query
-taxidlist 33090.txids -evalue 1.0e-5 -num_threads 23 -word_size 3 -max_target_seqs 1 -max_hsps 1 -outfmt 6 -out res_blastx
I got this error that " `Taxonomy ID(s) not found. ...
written 4 months ago by
m.s_tabatabaei • 0
• updated
4 months ago by
lieven.sterck ♦ 10k
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... Hi every one,
I am going to predict the target genes of miRNAs using psRNATarget. I am using a genome assembly consisting of long contigs as the scaffold and there isn't any GFF3 file for my plant species. The problem is that when the contigs, identified by psRNATarget, are subjected to BLASTX, a ...
written 6 months ago by
m.s_tabatabaei • 0
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... Hi Harshraje,
I have the same problem as your problem. I am working on small RNA data on plant in which there isn't any annotated reference genome for it. Could you please let me know if you got your answer. I am so thankful if you let me know which pipeline and tool you found to be good for plant ...
written 8 months ago by
m.s_tabatabaei • 0
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... Hi everyone,
I am working on small RNA seq on plant. Could you please guide me on which pipeline is better for plants without an annotated reference genome. which one of these tools" miRDeep2, miRDeep-p2, miRA" is the best or suggest me another one.
Thank you,
Mina
...
written 8 months ago by
m.s_tabatabaei • 0
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... Hi Tushar,
I am searching to find a good pipeline for plant small RNA seq. I worked with annotation and merge pipeline on CLC but I don't know which data in output should be considered as input to analyze differential expression. I worked with miRDeep2 as well but I am not sure it is good for plant ...
written 8 months ago by
m.s_tabatabaei • 0
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... Hi Tushar,
Could you please let me know which pipeline you found to small RNA seq analysis?
I am starting to analyze small RNA seq and your suggestion will help me a lot and I appreciate you a lot.
Thanks
...
written 10 months ago by
m.s_tabatabaei • 0
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... Hi every one,
I am starting to analyze small RNA data from **plants**. Could you please guide me on which pipeline is good? Is there any pipeline on the galaxy to use it?
How can I download Rfam data to identify and filter of noncoding RNAs from my data?
Thanks a lot for your guidance,
Mina ...
written 10 months ago by
m.s_tabatabaei • 0
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