User: archana.bioinfo87

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Posts by archana.bioinfo87

<prev • 107 results • page 1 of 11 • next >
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Comment: C: cannot make BLAST database using makeblastdb command line tool
... Dear, Check your input fasta file and also try to add DB name. What is your fasta file size? ...
written 15 hours ago by archana.bioinfo87170
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Comment: C: Aligning short oligos containing Ns to a genome
... Hi, If your file is not too big than you can try this command. Here your query sequence will act as a motif so it preserve "Ns" seqkit.exe locate --degenerate --ignore-case --pattern-file your_query.fa file_conatin_all_seq.fasta You can modify the command according to your requirement. H ...
written 24 days ago by archana.bioinfo87170
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Comment: C: How to make a loop to run kallisto bus command for so many fastq.gz files at onc
... You can also make two directory for R1 and R2 mkdir R1 mkdir R2 mv *R1_001.fastq.gz R1 mv *R2_001.fastq.gz R2 cd R1 ls | cat -n | while read n f; do mv "$f" "$n"_$f; done cd ../R2 ls | cat -n | while read n f; do mv "$f" "$n"_$f; done cd .. for i in $(seq 1 8 ...
written 28 days ago by archana.bioinfo87170
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Comment: C: How to interpret the Pan-Genome Result
... What tool or software you used for pan-genome analysis? What type of data you have used? If you can explain a little bit more about your work than it would be easy to answer your question. ...
written 28 days ago by archana.bioinfo87170
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Comment: C: extract subset of 21 nt. from csv file
... Thanks. I am going to try this as well. ...
written 5 weeks ago by archana.bioinfo87170
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Comment: C: extract subset of 21 nt. from csv file
... Thanks for your time and effort. I really appreciate it. ...
written 5 weeks ago by archana.bioinfo87170
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extract subset of 21 nt. from csv file
... Hi, I am trying to get 1-21nt, 2-22nt, 3-23nt etc till the end of sequences. For example, if I have sequences of 51 nt in length then I will get the 30 fragments with 21 nt in each fragment. I tried this script whcih looks to work fine but only for first 2 lines only. fasta <- read.csv( ...
R written 5 weeks ago by archana.bioinfo87170 • updated 5 weeks ago by JC9.1k
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Comment: C: remove NaNs from ExpressionSet
... Hi, try this code maybe it will work for you ExpressionSet[ExpressionSet == NaN] <- 0 ...
written 3 months ago by archana.bioinfo87170
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How to calculate essentiality score for circular RNA
... Hi, I am trying to find a way to calculate the essentiality score for circular RNA. What method I should use to calculate the score. Any help or suggestion is much appreciated. ...
R rna-seq written 3 months ago by archana.bioinfo87170
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Comment: C: Restrict GTF or GFF3 to final 3' exons
... you can do one more thing sort the data with respect to gene_id and for next in $(cut –d" “ -f1 sorted_data.csv | sort -u); do grep -w -m 3 "$next" sorted_data.csv ; done You can also modify the command according to your file columns. ...
written 4 months ago by archana.bioinfo87170

Latest awards to archana.bioinfo87

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