User: archana.bioinfo87

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Posts by archana.bioinfo87

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Comment: C: extract subset of 21 nt. from csv file
... Hi, I am getting extra space when gereratig the outfile from the perl script. I tried to mofiy it but space included in between in my sequences. As, you know previously I was trying from 1st position to last-21 nt but now I am looking for 1st to last+21nt (from 1-21 start position) Any help is m ...
written 15 months ago by archana.bioinfo87180
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Comment: C: Want read count with respect to geneID instead of transcript IDs
... I have one more query. Now as I have Ensembl gene IDs and I got the gene symbols with each Ensembl gene IDs. Also, I found that some Ensembl gene IDs having the same gene symbol. In this case, if I want read count w.r.t gene symbol then what I have to consider. Any help is much appriciated. Tha ...
written 15 months ago by archana.bioinfo87180
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Comment: C: Want read count with respect to geneID instead of transcript IDs
... Thanks for the help. ...
written 15 months ago by archana.bioinfo87180
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Comment: C: Want read count with respect to geneID instead of transcript IDs
... Thanks. I got the point. ...
written 15 months ago by archana.bioinfo87180
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Want read count with respect to geneID instead of transcript IDs
... Hi, Maybe my question is very basic but I just want to know how I will get the reads count with respect to geneID. I have RNA-seq data and I used htseq-count and got read count in terms of Ensembl Transcript ID. Thanks ...
forum rna-seq written 15 months ago by archana.bioinfo87180 • updated 15 months ago by lieven.sterck10k
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Comment: C: cannot make BLAST database using makeblastdb command line tool
... Hi dear, You can do a try for a small file first. And see will you able to make blastdb for that? If yes then do a cross-check again with your fasta file also check the empty fasta header. One more check you can do like empty lines in your file. Hoping these criteria check will help you. ...
written 15 months ago by archana.bioinfo87180
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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 months ago by archana.bioinfo87180
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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 16 months ago by archana.bioinfo87180
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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 16 months ago by archana.bioinfo87180
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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 16 months ago by archana.bioinfo87180

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