User: Pals

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Pals1.3k
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Finland
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animal genomics, cold adaptation ...

Posts by Pals

<prev • 121 results • page 1 of 13 • next >
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deseq dataset from star
... Hi, I have multiple count tables generated by star (using --quantMode). Is it possible to import these tables into deseq2 using DESeqDataSetFromHTSeqCount function or I need to create a matrix table and import using DESeqDataSetFromMatrix function? the tables look like this: N_unmapped 23994 ...
deseq2 star rna-seq written 17 months ago by Pals1.3k • updated 3 months ago by Biostar ♦♦ 20
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Comment: C: fastq file error
... Thanks a lot Brian and genomax2. I had also asked this problem to Jenya Kopylov (author of sortmerna) and I decided to skip sortmerna step for now. By the way, I found BBTools really useful :) ...
written 18 months ago by Pals1.3k
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Comment: C: fastq file error
... Here is the error from vpair step: /homeappl/home/kipokh/appl_taito/mytools/bbmap/reformat.sh in1=4563_END_sortmerna_R1.fastq.gz in2=4563_END_sortmerna_R2.fastq.gz vpair java -ea -Xmx200m -cp /homeappl/home/kipokh/appl_taito/mytools/bbmap/current/ jgi.ReformatReads in1=4563_END_sortmerna_R1.fa ...
written 18 months ago by Pals1.3k
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Comment: C: fastq file error
... While running the repair.sh ...
written 18 months ago by Pals1.3k
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Comment: C: fastq file error
... After the following error, the output file size is 3.1 compared to 3.3 (original). It seems sortmerna steps created the problem in reads. Started output stream. java.lang.AssertionError: Error in 4563_END_sortmerna_R2.fastq.gz, line 194876135, with these 4 lines: BBBFFFFFFFFFFIIIII ...
written 18 months ago by Pals1.3k
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fastq file error
... Hi, After removing rRNAs using sortmerna, 2/42 files failed fastqc with error: > uk.ac.babraham.FastQC.Sequence.SequenceFormatException: ID line didn't > start with '@' at > uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:158) > at uk.ac.babraham.FastQC.Sequence.Fast ...
fastq sortmerna rna-seq fastqc written 18 months ago by Pals1.3k
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Answer: A: What Is One Book Every Bioinformatician Should Read?
... Practical computing for biologists: http://practicalcomputing.org/ ...
written 5.0 years ago by Pals1.3k • updated 5.0 years ago by Malachi Griffith16k
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Comment: C: Suggestion For A Good Genome Center
... Thanks. In fact, my colleague is working with whole genome data sequenced in BGI China. However, he is not really satisfied with their primary analysis especially the choice of their tools. I will contact BGI considering advice from Alastair. ...
written 5.0 years ago by Pals1.3k
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Comment: C: Suggestion For A Good Genome Center
... Thank you very much for your advice! I will definitely consider these. ...
written 5.0 years ago by Pals1.3k
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Answer: A: What Do You Waste Your Time On
... Figuring out which tool to use. Lately, for analyzing miRNA data. Any pipeline suggestions? ...
written 5.0 years ago by Pals1.3k

Latest awards to Pals

Popular Question 18 months ago, created a question with more than 1,000 views. For How To Extract And Quantify Duplicated Rna-Seq Reads?
Popular Question 24 months ago, created a question with more than 1,000 views. For Bioinformatics Posters Collection
Great Question 24 months ago, created a question with more than 5,000 views. For Energy Minimization In Protein Modeling
Popular Question 24 months ago, created a question with more than 1,000 views. For How To Extract And Quantify Duplicated Rna-Seq Reads?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Parse Uniprot Fasta Record, Save It, Trim It And Quantify Each Residue
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Bioinformatics Posters Collection
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Building A Consensus Sequence From A Set Of Sequences
Popular Question 2.7 years ago, created a question with more than 1,000 views. For How To Extract And Quantify Duplicated Rna-Seq Reads?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Bioinformatics Posters Collection
Popular Question 2.7 years ago, created a question with more than 1,000 views. For How To Convert (Aligned) Text File Into An Alignment File?
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Source Of Predicted Genes In Ensembl
Popular Question 3.2 years ago, created a question with more than 1,000 views. For How To Extract And Quantify Duplicated Rna-Seq Reads?
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Properly Displaying Amino Acid Sequence Using Latex
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Building A Consensus Sequence From A Set Of Sequences
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Popular Question 3.5 years ago, created a question with more than 1,000 views. For How To Make A .Free Format Sequence Alignment File (For Matlab) ?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Source Of Predicted Genes In Ensembl
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Good Answer 4.0 years ago, created an answer that was upvoted at least 5 times. For A: How To Confirm The Presence Of 3D Structure Of A Small Molecule?
Good Question 4.0 years ago, asked a question that was upvoted at least 5 times. For Molecular Docking With Gold - How To Define A Ligand Binding Site?

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