User: Lina F

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Lina F50
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Boston, MA
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11 minutes ago
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2 years, 3 months ago
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Posts by Lina F

<prev • 28 results • page 1 of 3 • next >
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How to format input data for Picard CollectRnaSeqMetrics
... Hi all, I am trying to run Picard's CollectRnaSeqMetrics tool and noticed that my output contains a lot of zero values. I only get values for the following fields: PF_BASES -------------> 553934269 PF_ALIGNED_BASES -----> 552090508 RIBOSOMAL_BASES ------> 6920715 INTERGEN ...
gtf picard rna-seq written 20 minutes ago by Lina F50 • updated 13 minutes ago by Pierre Lindenbaum88k
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Comment: C: RNA-SeQC does not calculate information about "Strand Specificity"
... Thanks for the suggestion! I am actually using the [RNA-SeQC][1] tool from the Broad Institute; that's where the report came from. I will take a look at the tool you mentioned, maybe it will be more appropriate. [1]: http://archive.broadinstitute.org/cancer/cga/rna-seqc ...
written 8 days ago by Lina F50
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Answer: A: Classification of bacteria - bioinformatics
... I don't know if there is an easy ready-made answer for this question, but KEGG has a rudimentary "tree" of sorts: http://www.genome.jp/kegg/catalog/org_list.html You could download this html file and parse it and it will give you the links to genbank. Maybe Python's [beautifulsoup][1] module can h ...
written 8 days ago by Lina F50
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RNA-SeQC does not calculate information about "Strand Specificity"
... Hi all, I recently ran RNA-SeQC on yeast RNAseq data to assess the quality of the sequencing run. Unfortunately, the tool returned only "NA" for the "Strand Specificity" section: ![rnaseqc_strand_specificity_output][1] This sample contains single-end reads that I mapped to the reference using ST ...
qc rna-seq written 8 days ago by Lina F50 • updated 8 days ago by Charles Warden4.6k
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Comment: C: Yeast GTF file needed for RNA-SeQC run
... Ah, this makes sense -- thanks for the help! ...
written 9 days ago by Lina F50
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Yeast GTF file needed for RNA-SeQC run
... Hi all, I have some yeast RNAseq data and I would like to run RNA-SeQC to get an overview of the quality of the run. I got both the reference fasta sequence and the GTF file from Ensembl here: # fasta ftp://ftp.ensembl.org/pub/current_fasta/saccharomyces_cerevisiae/dna/Saccharomyces_cere ...
gtf qc yeast rna-seq rna-seqc written 9 days ago by Lina F50 • updated 9 days ago by apa@stowers320
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Comment: C: bwa mem: which parameters to tune to improve alignment?
... Thanks for the suggestion! I mapped with STAR, and it got rid of the sharp cutoffs and peaks which were probably splice sites: ![enter image description here][1] [1]: https://s28.postimg.org/wssvvbej1/Screen_Shot_2016_12_20_at_2_59_51_PM.png ...
written 4 weeks ago by Lina F50
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bwa mem: which parameters to tune to improve alignment?
... Hi all, I have a handful of genes of interest that I am trying to identify in a plant transcriptome dataset. I used bwa mem to map the paired-end transcriptome reads against a reference dataset generated from the genes of interest. The gene sequences I used as leads are not the same organism as t ...
parameters tuning bwa written 4 weeks ago by Lina F50
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Comment: C: Generating consensus sequences
... Thank you for the suggestion, I will try that! ...
written 6 weeks ago by Lina F50
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Generating consensus sequences
... Hi all, I am interested in generating consensus sequences from a bwa alignment. I generated the consensus sequences as follows: samtools mpileup -uf reference.fasta sorted.bam -d 8000 | bcftools call -mv -Oz -o sorted.vcf.gz tabix sorted.vcf.gz cat reference.fasta | bcftools consensus ...
consensus fasta vcftools bwa written 7 weeks ago by Lina F50 • updated 7 weeks ago by haro8730

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