User: Bioinfo

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Bioinfo120
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Posts by Bioinfo

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Comment: C: Creating Hisat2 Index
... If the alignment job fails then What should I do? Do I need build the index again. BTW I saw the sizes GRCh38_Hisat2_index.4.ht2 (703M), GRCh38_Hisat2_index.3.ht2 (12K), GRCh38_Hisat2_index.2.ht2 (0), GRCh38_Hisat2_index.1.ht2 (8K), GRCh38_Hisat2_index.8.ht2 (1.1K), GRCh38_Hisat2_index.7.ht2 (5K) ...
written 13 days ago by Bioinfo120
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Comment: C: Creating Hisat2 Index
... These are the files I got. Hisat2index.0.rf, Hisat2index.1.ht2, Hisat2index.2.ht2, Hisat2index.3.ht2, Hisat2index.4.ht2, Hisat2index.5.ht2, Hisat2index.6.ht2, Hisat2index.7.ht2, Hisat2index.8.ht2 Do you think this right? OR do I need to try with more memory and time. I gave 30 G and 6 h run time. ...
written 14 days ago by Bioinfo120
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Comment: C: Creating Hisat2 Index
... As you said I gave the run with 30G memory and more run time. The following is what I see: Output files: "Hisat2index.*.ht2" Line rate: 7 (line is 128 bytes) Lines per side: 1 (side is 128 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked L ...
written 14 days ago by Bioinfo120
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Comment: C: Creating Hisat2 Index
... Will give a try with this Thanks ...
written 14 days ago by Bioinfo120
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Comment: C: Creating Hisat2 Index
... Ok. I'm building index on cluster not on my desktop computer. ...
written 14 days ago by Bioinfo120
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Comment: C: Creating Hisat2 Index
... But I would like to build my own using the gtf ...
written 14 days ago by Bioinfo120
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Creating Hisat2 Index
... As mentioned in the [paper][1] I first extracted splice-sites and then exons. Next I used hisat2-build hisat2-build --ss gencode.v27.primary_assembly.annotation.ss --exon gencode.v27.primary_assembly.annotation.exon annot_AND_refFASTA/Homo_sapiens.GRCh38.dna.primary_assembly.fa Hisat2index Aft ...
genome hisat2 rna-seq index written 14 days ago by Bioinfo120
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Comment: C: Which strand specific option need to be used with HISAT2?
... Ok I got the answer from your old post [https://www.biostars.org/p/295344/] Thanks a lot for the help. ...
written 14 days ago by Bioinfo120
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Comment: C: Which strand specific option need to be used with HISAT2?
... Ok. I did the conversion. And used the infer_experiment.py This is what I see Total 9230 usable reads were sampled This is PairEnd Data Fraction of reads failed to determine: 0.0000 Fraction of reads explained by "1++,1--,2+-,2-+": 0.0047 Fraction of reads explained by "1+-,1-+,2++,2--": 0.9953 ...
written 14 days ago by Bioinfo120
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Comment: C: Which strand specific option need to be used with HISAT2?
... Yes, Thank you. I downloaded the gff3 file from gencode and In Galaxy (https://toolshed.g2.bx.psu.edu/) I dont see any gff3tobed converter. Could you please help me with this. ...
written 15 days ago by Bioinfo120

Latest awards to Bioinfo

Popular Question 28 days ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Popular Question 3 months ago, created a question with more than 1,000 views. For How to build Hisat2 index for human genome (GRCh37 )?
Centurion 5 months ago, created 100 posts.
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