User: AyehSadr

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AyehSadr0
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Posts by AyehSadr

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Comment: C: no alias or index file found for nucleotide database nr in search path error
... ls -l | head -n 20 total 452 drwxr-xr-x 2 fatemeh fatemeh 4096 Feb 28 11:19 nr.00 drwxr-xr-x 2 fatemeh fatemeh 4096 Feb 27 12:34 nr.01 drwxr-xr-x 2 fatemeh fatemeh 4096 Feb 27 12:40 nr.02 drwxr-xr-x 2 fatemeh fatemeh 4096 Feb 27 12:40 nr.03 drwxr-xr-x 2 fatemeh fatemeh 40 ...
written 3 months ago by AyehSadr0 • updated 3 months ago by jrj.healey13k
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Comment: C: no alias or index file found for nucleotide database nr in search path error
... the command is: blastx -query '/home/fatemeh/trinity_outp/Trinity.fasta' -db '/home/fatemeh/NCBI/nr' -out blastx.outfmt6 -evalue 1e-4 -num_threads 4 -max_target_seqs 1 -outfmt 6 ...
written 3 months ago by AyehSadr0
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Comment: C: no alias or index file found for nucleotide database nr in search path error
... I have this file in the directory that the files downloaded ...
written 3 months ago by AyehSadr0
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no alias or index file found for nucleotide database nr in search path error
... Dear All I have downloaded the nr database by this command wget 'ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr.*.tar.gz' and have extracted the files. When I run blastx I got this error: no alias or index file found for nucleotide database nr in search path. I would appreciate to guide me how I can fix ...
genome assembly alignment rna-seq sequencing written 3 months ago by AyehSadr0
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Comment: A: Identification of Long Non coding RNa in De novo
... Yes, 150 PE and transcriptome assembly process by means of Trinity ...
written 4 months ago by AyehSadr0
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Identification of Long Non coding RNa in De novo
... Dear All I am working on Identification of long non-coding RNAs in scorpion, in this case the genome reference is not available, I have to do blast for to all transcript candidates and I don't find the closest genome. I would appreciate to guide me about the best the best approach. Best Regards A ...
rna-seq written 4 months ago by AyehSadr0 • updated 3 months ago by Biostar ♦♦ 20
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Comment: C: Tophat Error "segment-based junction search failed"
... unfortunately  I couldn't find the problem, however I checked the segment-juncs run-log and tophat-log ...
written 4.0 years ago by AyehSadr0
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Tophat Error "segment-based junction search failed"
... Dear All I have  an error when run the tophat in some of samples, " segment-based junction search failed with err =-9 ". I would appreciate to guide me to solve it. [2015-06-14 03:30:56] Searching for junctions via segment mapping     [FAILED] Error: segment-based junction search failed with err = ...
software error next-gen rna-seq written 4.0 years ago by AyehSadr0 • updated 4.0 years ago by Sukhdeep Singh9.8k

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Popular Question 3.1 years ago, created a question with more than 1,000 views. For Tophat Error "segment-based junction search failed"
Autobiographer 4.1 years ago, has more than 80 characters in the information field of the user's profile.

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