User: kabir.deb0353

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Posts by kabir.deb0353

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Answer: A: How To Retrieve Hmmsearch Output Sequences From Target Database..
... Hello chevivien, Have you solved the problem? I'm facing the same problem and couldn't find any way out. It will be an immense help for me if you please give me suggestions to overcome it. Thanks in advance ...
written 8 months ago by kabir.deb03530
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Masking and Parsing problem in Standalone BLAST 2.7.1?
... Dear Sir/Ma'am, I was performing tBLASTn, Query = protein fasta sequence (n=114 ), Subject= Whole genome sequence In order to do that, I began with the building of a blast database after masking of sequence data using `dustmasker` and `windowmasker` $dustmasker -in XYZ.fna -infmt fasta -parse ...
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Comment: C: run_BUSCO.py running problem in UBUNTU-16.04?
... Thank yo so much @genomax for your suggestion, but now I'm stuck in the new problem, I was running BUSCO Command Line: python3 run_BUSCO.py --in ../sample_data/target.fa --out TEST --lineage_path ../sample_data/example --mode genome Error Message: INFO ****************** Start a BUS ...
written 8 months ago by kabir.deb03530
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run_BUSCO.py running problem in UBUNTU-16.04?
... I have installed BUSCO in my Ubuntu 16.04, according to the manual but when I run `run_BUSCO.py` it was showing line 26, in from pipebricks.PipeLogger import PipeLogger ModuleNotFoundError: No module named 'pipebricks' What should I do for solving this problem? ...
pipebricks busco written 9 months ago by kabir.deb03530
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Comment: A: How to Install Augustus properly ?
... No, I'm using python3. Is it mandatory to use bioconda! I really don't know. ...
written 9 months ago by kabir.deb03530
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How to Install Augustus properly ?
... I was trying to install Augustus in Ubuntu 16.04. However I have followed (http://bioinf.uni-greifswald.de/augustus/binaries/README.TXT) for installation but stuck in between the steps, -htslib -bcftools -tabix -samtools For bam2wig, these four packages must be installed from github. An installatio ...
augustus geneprediction busco written 9 months ago by kabir.deb03530 • updated 4 months ago by william.imart0
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Comment: A: htslib installation problem
... Thank you every one for the suggestions, the problem has been solved by using `sudo make install`. ...
written 9 months ago by kabir.deb03530
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htslib installation problem
... I was trying install htslib as dependencies for Auggustus. I have followed cd htslib/ autoheader autoreconf ./configure make make install I got stuck in the last step (make install); it was showing that, mkdir -p -m 755 /usr/local/bin /usr/local/include /usr/local/in ...
augustus busco htslib written 9 months ago by kabir.deb03530
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Extraction of batch subject sequence from Blast result.
... $ "~/ncbi-blast-2.5.0+/bin/makeblastdb" -in sub.fna -dbtype nucl -out sub_DB -parse_seqids $ "~/ncbi-blast-2.5.0+/bin/tblastn" -query que.fasta -db sub_DB -outfmt 6 -out result_0.01_out -evalue 0.01 -num_threads 24 $ "~/ncbi-blast-2.5.0+/bin/blastdbcmd" -db sub_DB -dbtype nucl -entry_batch entry_ ...
-entry_batch minus strand blastdbcmd written 9 months ago by kabir.deb03530 • updated 9 months ago by lieven.sterck4.2k
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Comment: C: How to extract start codon and stop codon from a fasta of multiple protein codin
... Yes, first 3 bases for Start codon and last 3, 2, or 1 base for the Stop codon; because some of the nucleotide seq have the cryptic stop codons. So the logic is that it will start count as 3 bases from beginning and print the first three letter of the sequence and then it will count upto to the seco ...
written 23 months ago by kabir.deb03530

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Popular Question 17 months ago, created a question with more than 1,000 views. For splitting Multifasta File Into A *Smaller Multifasta File containing few sequence

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