User: empyrean999

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empyrean999160
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Posts by empyrean999

<prev • 25 results • page 1 of 3 • next >
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Comment: C: modifying fasta header
... can you point me to some of your old suggestions? ...
written 3.2 years ago by empyrean999160
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Comment: C: modifying fasta header
... gene is not a static number and not in incremental order. The real file will have random descriptions of typical gene names . ...
written 3.2 years ago by empyrean999160
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modifying fasta header
... Hello; I need to process fasta header by matching fasta description (not fasta id) with a first column in a another file with two columns and print second column in file on to fasta header. Here are examples and what i have till now. file1.txt (list file) group_1 gene 1 group_2 gene 2 ...
perl fasta unix written 3.2 years ago by empyrean999160 • updated 3.2 years ago by 5heikki8.5k
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Comment: C: Normalizing small RNA Seq Reads
... The goal is to understand difference in num of reads mapping to that 5' region of gene approx (150bp) . REads only map to that part and no reads seen in rest of the gene. i have read counts only for that 150bp location . I wanted to see across different samples, what are the normalized read numbers ...
written 4.0 years ago by empyrean999160
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Normalizing small RNA Seq Reads
... Hello All, This could be a easy solution but just wanted to get your opinion on this. We have 10 different small RNA samples sequenced for arabidopsis. They are varied in read numbers from 10 million to 30 million . We wanted to look at reads mapping to 5' end of a gene. I used that gene as referen ...
normalization next-gen small rna rna-seq mirna written 4.0 years ago by empyrean999160
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Comment: C: Blast plus command line filter !
... thank you. i will look in to that ...
written 4.3 years ago by empyrean999160
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Blast plus command line filter !
... Hello All, I am doing blast with "NR" database which is taking very long time and i am interested in searching only specific species. Is there a way to submit in the blast option to restrict it to search for specific species. I am using blast plus. In older blast there is command "blastall -u "orga ...
command line unix blast written 4.3 years ago by empyrean999160 • updated 3.7 years ago by Biostar ♦♦ 20
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Comment: C: How To Add Specific Word To First word in Fasta header
... True but i need -parse_seqids to extract sequences from fasta file.  ...
written 4.5 years ago by empyrean999160
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How To Add Specific Word To First word in Fasta header
... I have fasta file with different headers. Basically assembled fasta files some are assembled with different versions so they got same fasta names. When i tried to make a blast database with "-parse_seqids" its complaining me of duplicate id's. So i would like to add a extension to with version of as ...
perl sed unix awk written 4.5 years ago by empyrean999160 • updated 4.5 years ago by Frédéric Mahé2.9k
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Comment: C: Modifying fasta header
... The space thing worked. Thanks for the tip. I just substituted in vim using space . Unfortunately i cannot change the upstream flow as this itself is starting file which was given to me. ...
written 5.1 years ago by empyrean999160

Latest awards to empyrean999

Great Question 3.6 years ago, created a question with more than 5,000 views. For Filtering Fastq Sequences Based On Lengths
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Filtering Fastq Sequences Based On Lengths
Student 4.5 years ago, asked a question with at least 3 up-votes. For Archiving/Documentation For Ngs Projects
Popular Question 5.1 years ago, created a question with more than 1,000 views. For Filtering Fastq Sequences Based On Lengths
Popular Question 5.1 years ago, created a question with more than 1,000 views. For Remove Redundant Sequences Fasta
Popular Question 5.5 years ago, created a question with more than 1,000 views. For Filtering Fastq Sequences Based On Lengths
Student 5.5 years ago, asked a question with at least 3 up-votes. For Archiving/Documentation For Ngs Projects
Student 5.5 years ago, asked a question with at least 3 up-votes. For Extract Fasta Sequences Using Wild Card Search

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