User: shaun

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shaun80
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Location:
Israel
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3 years, 6 months ago
Joined:
3 years, 10 months ago
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Posts by shaun

<prev • 9 results • page 1 of 1 • next >
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Answer: C: motif detection analysis
... FANMOD is for detecting *network* motifs, I guess you would like to detect *sequence* motifs. You better use MEME suite in which case just give it the DNA/protein sequence of you genes/promoters (depending on your interest). ...
written 3.7 years ago by shaun80
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Comment: C: Join mapped, overlapping, paired-end reads
... Why would you like to do that? Maybe there are other ways to reach your goal ...
written 3.7 years ago by shaun80
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Comment: C: How to extract sequence from fasta file with specific coordinates?
... python seq_ext_coordinate.py fasta_file.fa blast_out.txt fasta_file.fa - fasta file you want to cut the sequences from blast_out.txt - output file of blast (see that format matches the script, I think -outfmt 6) ...
written 3.7 years ago by shaun80
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Answer: A: How to extract sequence from fasta file with specific coordinates?
... The script is expecting the fasta file name as first argument and the position as second argument. ...
written 3.7 years ago by shaun80
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Comment: C: RNA-Seq from limited cells
... The major problem in this analysis is the high amount of noise. One way to reduce it is using UMI's like in here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4412462/ . Another option is to have a lot of replicates to better estimate dispersion. Use DESeq2 to get DE genes, if neither of the above we ...
written 3.7 years ago by shaun80
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Answer: A: Does BWA (BWA-MEM) care about the identity and coverage of the mapped reads?
... You can tweak these features with the -B (mismatch penalty) -O and -E (gap penalties). You can see the coverage and mismatches in the resulting bam file and post-process it if you think the results are unsatisfying using samtools for instance. ...
written 3.7 years ago by shaun80
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Answer: A: map bed file to other bed file
... bedtools http://bedtools.readthedocs.io/en/latest/ (intersect bed) ...
written 3.7 years ago by shaun80
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Answer: A: cell annotation question - rnaseq
... Obvious approach - check if genes with differential expression are markers (example - CD4 == T-lymphocyte). another approach is search for cell expression profile database (for example http://www.ebi.ac.uk/gxa/baseline/experiments) and compare profiles of your experiment with database, look for too ...
written 3.7 years ago by shaun80
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Answer: A: Best way to determine gene positions in a related strain, from a well annotated
... You can use CDS and/or proteins from A. thal ecotype (Col) as input for BLAT against your genome. Map the RNAseq to validate "BLAT based " gene models. Use cufflinks to compare the models. ...
written 3.8 years ago by shaun80

Latest awards to shaun

Scholar 3.7 years ago, created an answer that has been accepted. For A: map bed file to other bed file
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: map bed file to other bed file

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