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No change in number of reads and quality after removing rRNA contamination using sortmerna

seqmonk sortmerna rna-seq fastqc written 5 hours ago by Sumit Paliwal • 20

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129

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RNA Seq data network analysis

rna-seq written 17 hours ago by chetana • 10 • updated 13 hours ago by kennethcondon2007 • 790

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111

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betweenLaneNormalization and calcNormFactors in RUVs

R ruvs rna-seq differential gene expression written 1 day ago by manish20072013 • 0

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124

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two transcriptomes, same RNAseq, different results. why?

rna-seq transcriptome written 17 hours ago by rm5585 • 0

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101

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goseq analysis with only geneid or genesymbol

R rna-seq written 19 hours ago by novicebioinforesearcher • 20

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160

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tophat 2 rna seq

rna-seq written 8 weeks ago by dimitrischat • 30 • updated 21 hours ago by Oskar • 20

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178

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How and what are the steps for performing RNAseq Time point analysis 3 biological replicates and 4 Technical replicates for each

time point rna-seq written 1 day ago by macmath • 110 • updated 23 hours ago by Michael Dondrup ♦ 42k

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Scholar to Pierre Lindenbaum ♦ 95k
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Recent Replies

C: Extension of reads by genomax ♦ 29k
How do i also extend with high quality score? Can I ask this? Why are you fascinated with ge...
C: FASTQ- Reverse reads of paired end sequence worse than forward reads by genomax ♦ 29k
See Illumina tech support's answer quoted by @Paul [in this thread][1]. Scores as high as 45 are ...
C: FASTQ- Reverse reads of paired end sequence worse than forward reads by genomax ♦ 29k
To get the original illumina read ID's try `fastq-dump` with `-F` option.
C: spliting sdf file by WouterDeCoster ♦ 19k
It would be definitely helpful if you show a snippet of how your file looks like - you can't expe...
A: Run Samtools on multiple files by WouterDeCoster ♦ 19k
Using gnu parallel in its simplest form: ls *.bam | parallel -j 8 'samtools sort -@ 7 {} &g...
C: Run Samtools on multiple files by Vijay Lakhujani • 930
On a separate note, this is really cool, suggestions to learn how to use "make" (tutorial links) ...
C: Run Samtools on multiple files by Vijay Lakhujani • 930
May be I am asking silly question, does that "16" means the no. of threads?
C: Run Samtools on multiple files by Vijay Lakhujani • 930
+1 Thanks venu for the suggestion, though I am clueless why the loop I suggested does not work fo...
C: FASTQ- Reverse reads of paired end sequence worse than forward reads by dilawerkh4 • 0
Hi Brian, These are the 1st few lines from the fastq generated with fastq-dump from SRA. What do...
A: Run Samtools on multiple files by Pierre Lindenbaum ♦ 95k
create the following '**Makefile**' SHELL=/bin/bash BAMS=$(shell ls -1 *.bam) define...
C: Run Samtools on multiple files by venu • 3.9k
Just a comment, when you are defining output filename, it's always better to use `basename` in or...
C: goseq analysis with only geneid or genesymbol by Devon Ryan ♦ 68k
Look at what goseq needs as input. Compare that to what you have. Make up constant numbers for th...

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