User: jaqx008

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jaqx00840
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1 year, 1 month ago
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Posts by jaqx008

<prev • 212 results • page 1 of 22 • next >
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Comment: C: Looking for recommendations: Transposon and evolution.
... So I have an small RNA seq data and have identified small RNAs that map to and would possibly control TEs in the basal organism, My thought is, the TE populations that are not being repressed could have resulted in the evolution of the vertebrate if that makes sense. So I am exploring other analysis ...
written 12 days ago by jaqx00840
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Comment: C: How to generate bed from fasta.
... It was resolved on that post, Thanks ...
written 12 days ago by jaqx00840
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Comment: C: How can I make a .bed file from my fasta?
... This worked fine for what I wanted. Thanks ...
written 12 days ago by jaqx00840
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Comment: C: How to generate bed from fasta.
... That post solved it I think by giving the length of the sequence. I actually want coordinates mapped to the reference genome this time if that makes sense. Thanks ...
written 14 days ago by jaqx00840
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(Closed) How to generate bed from fasta.
... Hello Everyone, I have a fasta file and need to generate bed file that will contain start and stop position of each read. I do have a genome file for my organism but don't know what command to use. Thanks ...
fasta bed bedtools genome written 14 days ago by jaqx00840
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Comment: C: How can I make a .bed file from my fasta?
... How can this be done? I have a fasta file and I need to get the bed cordinates that will have start and stop positions as mapped to the genome. ...
written 14 days ago by jaqx00840
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Comment: C: Where can I obtain Transposable elements of Zebra fish (Danio)
... Thanks. However, this is a fasta file. I am looking for a file with all TE classes specified. example is shown below Bf_V2_1 1 797 - bf_rep_71 Unknown Bf_V2_1 848 936 + (TA)n Simple_repeat Bf_V2_1 1236 1369 - CR1-11_BF LINE/CR1 Bf_V2_1 ...
written 14 days ago by jaqx00840
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Where can I obtain Transposable elements of Zebra fish (Danio)
... Hello All, Can anyone recommend a link Where I can get a file with Transposable elements for zebrafish? Thanks ...
genome transposones zebrafish written 15 days ago by jaqx00840
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Comment: C: BedtoBam error: Why is this?
... I was able to get the bam by first getting the genome file (from the command below) that has only chr name and length then using this in the bedtobam command. cat file.fa | awk '$0 ~ ">" {print c; c=0;printf substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END { print c; }' > xx.gen ...
written 6 weeks ago by jaqx00840
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Comment: C: BedtoBam error: Why is this?
... The usage says -g . then it say fai should work with bedtools in the documentation ...
written 6 weeks ago by jaqx00840

Latest awards to jaqx008

Popular Question 4 weeks ago, created a question with more than 1,000 views. For Split BAM file.
Supporter 6 weeks ago, voted at least 25 times.
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Split BAM file.
Popular Question 10 weeks ago, created a question with more than 1,000 views. For RuntimeError: dictionary changed size during iteration
Popular Question 4 months ago, created a question with more than 1,000 views. For python script error: ImportError: No module named pysam
Scholar 6 months ago, created an answer that has been accepted. For A: GREP: out of memory
Centurion 8 months ago, created 100 posts.
Rising Star 10 months ago, created 50 posts within first three months of joining.

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