Moderator: Asaf

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Asaf4.5k
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Israel
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Posts by Asaf

<prev • 514 results • page 1 of 52 • next >
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Comment: C: Bacterial genome annotation
... Are you sure you used prokka properly? You can specify a blast database to make predictions more accurate. I would have suggested prodigal for gene annotation but it's included in prokka ...
written 2 days ago by Asaf4.5k
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Comment: C: Tophat alignments is low but STAR is high.
... Sounds right. You can look at some reads that were mapped by STAR but not by tophat and see how many mismatches they have ...
written 6 days ago by Asaf4.5k
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Answer: A: Motif seq in input seq and genes
... MEME can be used to (re)identify the motif and evaluate its statistical significance. MAST can be then used to search for the motif in other regions of the genome. http://meme-suite.org/ ...
written 7 days ago by Asaf4.5k
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Comment: C: non-coding RNAs target predictions
... Are you certain about the mechanism being direct interactions with mRNAs? ...
written 7 days ago by Asaf4.5k
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Comment: C: problem with the alignment of RNAseq data
... It's hg19. Mentioned in the question. In addition try to count the number of reads mapped to the genome. ...
written 8 days ago by Asaf4.5k
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Comment: C: Compare RNAseq Data from two independent runs?
... I don't know. You can ask for the specific protocol (you'll need it anyway). In addition, you can plot the samples using PCA to see if the second batch cluster together or with their biological relatives. ...
written 8 days ago by Asaf4.5k
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Answer: A: Compare RNAseq Data from two independent runs?
... 1. Try to figure out if the library preparation protocol was different between the batches, if it was indeed different that's not good. 2. You can correct for batch effect in DESeq2 ...
written 9 days ago by Asaf4.5k
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Comment: C: Bacterial RNA-seq analysis
... You woke-up an old discussion, I think it would be better to open a new post describing your experiment and obstacles. ...
written 9 days ago by Asaf4.5k
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Comment: C: From evidence-based alignments on de-novo assembly, to gene identification
... Prodigal will give you the coding regions while the RNA-seq results will give you the transcripts, including ncRNAs. If you'll combine them you'll get the genes with the UTRs. I'm not aware of a tool that does this combination neatly, bedtools might be a good tool to get the ORFs from prodigal align ...
written 9 days ago by Asaf4.5k
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Comment: C: From evidence-based alignments on de-novo assembly, to gene identification
... Unfortunately no. I'm not aware of a good public tool for eukaryotes. ...
written 13 days ago by Asaf4.5k

Latest awards to Asaf

Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: What to do after an genome assembly?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How To Mark Specific Species On The Tree Of Life?
Scholar 7 weeks ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Appreciated 5 months ago, created a post with more than 5 votes. For A: How To Mark Specific Species On The Tree Of Life?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How To Mark Specific Species On The Tree Of Life?
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: What to do after an genome assembly?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How To Mark Specific Species On The Tree Of Life?
Popular Question 6 months ago, created a question with more than 1,000 views. For Getting transcripts from BAM file with gene names
Popular Question 6 months ago, created a question with more than 1,000 views. For Getting transcripts from BAM file with gene names
Scholar 8 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How To Mark Specific Species On The Tree Of Life?
Popular Question 11 months ago, created a question with more than 1,000 views. For Counting reads for gene in bacterial genomes
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Find Enriched Function In Go Terms
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Find Enriched Function In Go Terms
Popular Question 13 months ago, created a question with more than 1,000 views. For What Do You Waste Your Time On
Scholar 13 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Scholar 14 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Scholar 14 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Scholar 14 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Scholar 14 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Scholar 14 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Find Enriched Function In Go Terms
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Find Enriched Function In Go Terms
Scholar 15 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Find Enriched Function In Go Terms

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