User: arunprasanna83

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Posts by arunprasanna83

<prev • 41 results • page 1 of 5 • next >
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Comment: C: Remove gene features from a given list
... the problem is, it will remove all the lines with g1 but leaves the traces like lines from # protein sequence till # W: 14. This would make the gff3 file untidy. ...
written 3 months ago by arunprasanna8330
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Remove gene features from a given list
... Hello, Is there a tool that can help me remove the entire features for a given list of genes? i.e from this gff3-version, I want to remove all the features related to g1 (start to end). # start gene g1 scaffold1size1833262 AUGUSTUS gene 1 1168 0.56 + . ID=g1 scaffold1size1833262 AUGU ...
gene annotation gff3 written 3 months ago by arunprasanna8330
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filter gff3 file for complete gene
... I have a gff3 file which has complete length sequence. But, few of the complete sequences have multiple UTRs. I wish to filter them out. Is there any utility that is available ? > scaffold105size588288 transdecoder gene 130390 132407 . + . > scaffold105size588288 transdecoder mRNA 130390 132 ...
genome assembly next-gen written 3 months ago by arunprasanna8330 • updated 9 weeks ago by Juke-342.4k
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Answer: A: annotate gene feature
... It is for multiple purpose. This is basically a isoseq data. So need to confirm how many of them are full length transcripts. ...
written 4 months ago by arunprasanna8330
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annotate gene feature
... Hi, I have a multi-fasta file with >15k DNA sequences. I wish to mark, UTR's, start, stop features. I tried expasy translate tool and it gives translated sequence with different possible ORFs. My objective is to find, how many sequences are full length. Kindly suggest. Thanks. ...
gene annotation feature utr written 4 months ago by arunprasanna8330
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Estimate insert size for pacbio long reads
... I am trying to use pacbio long reads to do gap filling using GapFiller program. What is the correct way of specifying the insert size mentioned in library file ? In other words, how to estimate insert size for pacbio long reads (SMRT). Thanks in Advance. ...
assembly next-gen gapfilling written 7 months ago by arunprasanna8330
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Comment: C: Troubleshooting assembly contigs of large genome
... I am using mummer 3.2.3. As @gconception mentioned I will try 4. How does blastn help ? ...
written 11 months ago by arunprasanna8330
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Comment: C: Troubleshooting assembly contigs of large genome
... I used mummer 3.2.3. I will give 4 a try !. Btw. D-GENIES web version failed and a local installation is not friendly. The assemblies are from long reads and assembled with Canu. ...
written 11 months ago by arunprasanna8330
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Troubleshooting assembly contigs of large genome
... Hello, Following is my strange situation: I assembled genomes from same sample (haploid source) with two different methods. Assembly size of two methods are the following: Method1 = 900 Mb (5400 contigs >10kb) Method2 = 500 Mb (7000 contigs >10kb) I suspected duplication in Method 1 and ch ...
genome assembly alignment sequencing written 11 months ago by arunprasanna8330
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Comment: C: Visualizing contig alignment
... As I mentioned in comments above, AliTV is also working fine for smaller files. But for bigger files it is taking forever. I guess there is no parallelization option. ...
written 11 months ago by arunprasanna8330

Latest awards to arunprasanna83

Popular Question 3 months ago, created a question with more than 1,000 views. For Motif prediction with MEME
Scholar 3 months ago, created an answer that has been accepted. For A: annotate gene feature
Popular Question 7 months ago, created a question with more than 1,000 views. For Motif prediction with MEME

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