User: debitboro

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debitboro180
Reputation:
180
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Belgium
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5 years, 12 months ago
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Posts by debitboro

<prev • 80 results • page 1 of 8 • next >
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Answer: C: How to append two fastq files ?
... I got it, simply: paste -d '\n' file2.fastq file1.fastq | sed -n 'p;n;n;N;s/\n//p' > result.fastq Thank you h.mon for you help ...
written 6 months ago by debitboro180
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Comment: C: How to append two fastq files ?
... I want to concatenate only the read sequences and quality sequences not all the components of a record. I need to do that to adapt my file as an input for in-house script for UMI deduplication. ...
written 6 months ago by debitboro180
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Comment: C: How to append two fastq files ?
... Thank you for your answer, but that is not what I'm looking for. I think the question is clearly formulated: I need to prefix the reads of the first file with the reads of the second file. ...
written 6 months ago by debitboro180
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How to append two fastq files ?
... Dear Biostars, How can I append sequences of two fastq files ? Suppose we have two fastq files: **file1.fastq** @HEADER CTCAGNTTGG + AAAAA#EEEE @HEADER GTGAGTTTAG + AA ...
fastq append merge rna-seq written 6 months ago by debitboro180
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positive and negative Fold Change glmLRT test
... Dear Biostars, I've a RNAseq counts dataset of 32 samples belonging to two groups: group1 (16 samples) and group2 (16 samples). Each group contains 2 subgroups: subgroup1 (8 samples), and subgroup2 (8 samples). Now, by using glmLRT test I want to find deferentially expressed genes between subgroups ...
log2fc glmlrt rna-seq differential expression written 13 months ago by debitboro180
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Comment: C: short RNA reads alignment
... I mapped my reads against Human genome (Homo_sapiens.GRCh38.dna.primary_assembly.fa). Did you mean my reads are contaminated by rRNA sequences ? ...
written 2.1 years ago by debitboro180
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Comment: C: short RNA reads alignment
... Hi genomax, Thank you for your suggestion, I've used BBMap with the values of parameters as you suggested, and I got the following results (I used another sample different from the one used for STAR alignment, but both of them are generated using the same protocol): ------------------ Res ...
written 2.1 years ago by debitboro180
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Comment: C: All my reads fall in intergenic regions ?
... Since the length of my reads is distributed between 22-50 nt, I think it is clear I got a high rate of multiple mapped reads. A very short read of 25 nt will get a higher number of multiple aligned locations on the genome than a read of a higher length. I am right ? ...
written 2.1 years ago by debitboro180
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Comment: C: All my reads fall in intergenic regions ?
... >80% rRNA even if rRNAs have been removed during the experiment with rRNA depletion kit ? ...
written 2.1 years ago by debitboro180 • updated 2.1 years ago by RamRS27k
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Comment: C: All my reads fall in intergenic regions ?
... It is total RNAseq experiment. The sequencing has been done on degraded RNA samples (single-end) and with a particular library preparation protocol, that is why I got very short RNAseq reads. We don't target any class of RNAs. ...
written 2.1 years ago by debitboro180

Latest awards to debitboro

Popular Question 7 weeks ago, created a question with more than 1,000 views. For SNP: direction of effects
Student 7 weeks ago, asked a question with at least 3 up-votes. For RNA-Seq for DE analysis
Popular Question 4 months ago, created a question with more than 1,000 views. For RNA-Seq Mapping and bowtie2 indexing
Popular Question 4 months ago, created a question with more than 1,000 views. For SNP: direction of effects
Great Question 8 months ago, created a question with more than 5,000 views. For Cleaning RNA-Seq data from rRNA
Popular Question 8 months ago, created a question with more than 1,000 views. For Tophat2 error when mapping using -G option
Popular Question 8 months ago, created a question with more than 1,000 views. For RNA-Seq Mapping and bowtie2 indexing
Popular Question 8 months ago, created a question with more than 1,000 views. For SNP: direction of effects
Epic Question 9 months ago, created a question with more than 10,000 views. For Cleaning RNA-Seq data from rRNA
Popular Question 9 months ago, created a question with more than 1,000 views. For Cufflinks: exceeded memory limit (31836604 > 31457280), being killed
Popular Question 9 months ago, created a question with more than 1,000 views. For Tophat2 error when mapping using -G option
Popular Question 14 months ago, created a question with more than 1,000 views. For Cufflinks: exceeded memory limit (31836604 > 31457280), being killed
Popular Question 14 months ago, created a question with more than 1,000 views. For Tophat2 error when mapping using -G option
Popular Question 14 months ago, created a question with more than 1,000 views. For RNA-Seq Mapping and bowtie2 indexing
Great Question 15 months ago, created a question with more than 5,000 views. For Cleaning RNA-Seq data from rRNA
Popular Question 16 months ago, created a question with more than 1,000 views. For Gene length table from gtf file for rpkm() function
Popular Question 16 months ago, created a question with more than 1,000 views. For Gene length table from gtf file for rpkm() function
Popular Question 17 months ago, created a question with more than 1,000 views. For Gene length table from gtf file for rpkm() function
Scholar 18 months ago, created an answer that has been accepted. For A: Bug in RUV spike-in normalization?
Scholar 18 months ago, created an answer that has been accepted. For A: Bug in RUV spike-in normalization?
Popular Question 19 months ago, created a question with more than 1,000 views. For Gene length table from gtf file for rpkm() function
Popular Question 19 months ago, created a question with more than 1,000 views. For Cufflinks: exceeded memory limit (31836604 > 31457280), being killed
Popular Question 19 months ago, created a question with more than 1,000 views. For Gene length table from gtf file for rpkm() function
Popular Question 19 months ago, created a question with more than 1,000 views. For Gene length table from gtf file for rpkm() function
Popular Question 19 months ago, created a question with more than 1,000 views. For Cufflinks: exceeded memory limit (31836604 > 31457280), being killed

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