User: backmoons

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Posts by backmoons

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Comment: C: DESeq2 to do differential expression analysis for multiple groups
... Hi, Thanks for your kind reply! so it means I need to use "time" as another "condition"? (I read some manual but still a little confused, this will help us find the genes waved with times or..? if compared this way with normal differential expression analysis without time course.) And I also have a ...
written 5 months ago by backmoons0
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DESeq2 to do differential expression analysis for multiple groups
... Dear all, I got a matrix from the last step(htseq count), and I need to do differential expression using that. My species is a fish, and the aim is to find the genes related to the air-breathing organ. I have 7 time-point for development stages with two replicates, here is my code for DESeq2, but i ...
R rna-seq sequencing written 5 months ago by backmoons0 • updated 5 months ago by Philipp Bayer6.3k
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Comment: C: samtools sort truncated
... Hi, Thanks for your kind reply. you mean "--outSAMtype BAM Unsorted "this parameter in STAR? yes, maybe I can( I will try it later). but I tried to don't use this parameter just now the output is sam file, then I use "samtools view" to convert the sam file to bam file, same error. What I afraid is ...
written 5 months ago by backmoons0
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Comment: C: samtools sort truncated
... Sorry I am very new to this, what do you mead by offending read(s)... :( ...
written 5 months ago by backmoons0
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samtools sort truncated
... Dear all, I meet a problem when I analyzed the RNA-seq data using STAR-HESeq count pipeline, when I finished STAR, and got a bam file, I used "samtools sort" to sort the data, but I got an error: **[E::bam_read1] CIGAR and query sequence lengths differ for GWNJ-0842:379:GW1810081505:6:2106:295 ...
rna-seq written 5 months ago by backmoons0 • updated 5 months ago by finswimmer11k
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Comment: C: transcriptome with and without reference genome
... Hi, I think this makes sense! But I am a little confused with step2, after finding the differential expressed genes within each species, we need to do the compared the homology genes? could you please give me more details about the step2..Appreciate it! ...
written 8 months ago by backmoons0
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transcriptome with and without reference genome
... Dear all, I am new to bioinformatics and have a question for my project. I have three species that have close relationships, one species has a reference genome (I used hisat2 for this), other two species haven't had a reference genome, each species have about 7 time-point. I assembly the two specie ...
genome rna-seq written 8 months ago by backmoons0 • updated 8 months ago by WouterDeCoster40k

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