User: Picasa

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Picasa310
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Posts by Picasa

<prev • 212 results • page 1 of 22 • next >
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Filter transcripts based on expression value: TPM vs TMM ?
... Hello, I have a transcriptome that I would like to filter by expression value. Basically, I have 3 samples that I mapped against my transcriptome with kallisto. I have then use Trinity tool (abundance_estimates_to_matrix.pl) to produce an expression matrix, which gave me 2 matrix: - a matrix of ...
transcriptome tpm tmm written 3 days ago by Picasa310
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Cutoff for TPM value
... Hi, I need to filter my transcriptome to speed up some process. I will map my samples against my transcriptome and compute the TPM value per contig per sample. Do you have an idea about which minimum TPM value I should use if any sample has it ? ...
tpm transcriptome written 7 days ago by Picasa310
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Comment: C: Converting PE to SE
... Thanks for your answer, but I need to be sure that I understand how R2 is : the reverse complement or only reverse ? ...
written 14 days ago by Picasa310
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Converting PE to SE
... Hello, I have RNAseq paired end in fr-firststrand (as described here http://chipster.csc.fi/manual/library-type-summary.html). I have also RNA reads in single end (reverse orientation). I need to perform a mapping but since it cannot handle a mix of PE and SE, I have to transform my PE into SE ( ...
pe se written 14 days ago by Picasa310
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Comment: C: Extract all paired reads from sam file
... Thanks, It looks like to work. Just a quick question: if a read is present and its mate has been excluded, with your command, does it remove the paired or reinclude the mate ? ...
written 4 weeks ago by Picasa310
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Extract all paired reads from sam file
... Hi, I had to filter manually a sam file by keeping only reads that fall into a specific regions. Using flagstat, my sam file is looking like this now: 160995 + 0 in total (QC-passed reads + QC-failed reads) 1148 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 159950 + 0 map ...
paired sam written 4 weeks ago by Picasa310 • updated 4 weeks ago by ATPoint1.7k
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Extract reads from specific target in .bam file
... Hi all, I am looking to extract reads that are mapped to a specific target. Let's say I have a file target.txt like this: > **head target.txt** > > scaffold1 > > scaffold2 > > scaffold3 And an another file which is a bam file. Is there a tool that extract reads (or filte ...
filter bam written 5 weeks ago by Picasa310
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MAKER annotation post processing (AED score)
... Hi, I have successfully annotated my genome with MAKER. Now I have a gff file that I want to post process /filter. In particular, I would like to discard gene that is below a certain AED score. 1) Is there an AED treshold from where a gene is not strongly supported ? if yes, do you have some refe ...
aed maker written 3 months ago by Picasa310 • updated 4 weeks ago by dfajar210
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Answer: A: Error For End Coordinate When Running Cuffdiff
... I have the same error even without using the -s in cuffmerge ... any solution ? ...
written 4 months ago by Picasa310
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Comment: C: Using RNA seq for genome annotation
... Well Maker needs (not mandatory but recommended) transcriptome to infer gene with gene predictor. ...
written 4 months ago by Picasa310

Latest awards to Picasa

Popular Question 10 days ago, created a question with more than 1,000 views. For Coverage per contig from a BAM file
Popular Question 12 weeks ago, created a question with more than 1,000 views. For LD pruning and other QC before association analysis ?
Popular Question 3 months ago, created a question with more than 1,000 views. For PCA on VCF
Popular Question 8 months ago, created a question with more than 1,000 views. For Best strategy for de novo assembly with illumina reads ?
Popular Question 8 months ago, created a question with more than 1,000 views. For Best strategy for de novo assembly with illumina reads ?
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Student 13 months ago, asked a question with at least 3 up-votes. For Best strategy for de novo assembly with illumina reads ?
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Scholar 15 months ago, created an answer that has been accepted. For A: 16S Paired-End Illumina MiSeq Data in Qiime
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