User: archana.bioinfo87
archana.bioinfo87 • 180
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Posts by archana.bioinfo87
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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 8 months ago by
archana.bioinfo87 • 180
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... 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 8 months ago by
archana.bioinfo87 • 180
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... Thanks for the help. ...
written 8 months ago by
archana.bioinfo87 • 180
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... Thanks. I got the point. ...
written 8 months ago by
archana.bioinfo87 • 180
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5 follow
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... 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 ...
written 8 months ago by
archana.bioinfo87 • 180
• updated
8 months ago by
lieven.sterck ♦ 8.3k
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... 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 8 months ago by
archana.bioinfo87 • 180
0
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... Dear,
Check your input fasta file and also try to add DB name. What is your fasta file size? ...
written 9 months ago by
archana.bioinfo87 • 180
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... 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 9 months ago by
archana.bioinfo87 • 180
0
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... 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 10 months ago by
archana.bioinfo87 • 180
0
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... 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 10 months ago by
archana.bioinfo87 • 180
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