User: shl198
shl198 • 380
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Posts by shl198
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Comment:
C: Augustus install mac
... Just thought it may be useful to others, I put my comment here. In my case, gcc version also matters. gcc4.8 works for bam2hints but not filterbam. I used gcc5.4 to compile filterbam successfully. ...
written 3.7 years ago by
shl198 • 380
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... Dear all,
I searched some threads, it seems like the standard recommendation for doing differential expression analysis is that: merge the fastq files of technical replicates together and then map to reference, count reads, do DE analysis. .
My question is that will it be safer if we map, count a ...
written 5.2 years ago by
shl198 • 380
• updated
5.2 years ago by
Antonio R. Franco • 4.5k
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... I wonder what is the relationship between the depth and gene expression level in RNAseq?
For example, let's say I have RNAseq with 10M reads for one sample. If I use the same machine and generate 20M reads for the same sample, then except for the new detected genes, will the expression profile for ...
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... Thanks. Yes, there is coding variants, but provean also needs the whole protein sequence, After building the database using snpeff, there is only one .bin file, do you know how to get the whole protein sequence? The only way I can think of is using genome annotation file, but it would be a little bi ...
written 5.6 years ago by
shl198 • 380
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... Hi all,
I called variants using GATK, and annotated the results using snpeff. Since the organism is chinese hamster, there is not much information available. I want to use provean to predict the effects of variants. The problem is that the input for provean for non human/mouse model should be amino ...
written 5.6 years ago by
shl198 • 380
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... Hello all,
I find a problem that interest me. The chinese hamster genome was assembled using DNAseq. And when I tried to use the same DNAseq to call SNPs, it detected some SNPs. My question is: the assembly should not change the sequence, so there should be no SNPs if I use the same DNAseq which wa ...
written 5.8 years ago by
shl198 • 380
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... Hi, I just wonder how you get the information of
Molecule Type:mixed DNA
Update date:2014/07/24
Number of sequences:23840180.
And also the number of bases? Thanks.
...
written 6.0 years ago by
shl198 • 380
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... Thank you very much. I will try STAR.
...
written 6.0 years ago by
shl198 • 380
0
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1
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2.3k
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... Hi Devon, thank you very much. I just tried mapping using bowtie2 directly instead of tophat, the result increased a little, and I also blast the unmapped reads, most of them mapped to mouse ribosomal RNA.
I didn't change the annotation file, and I made sure there are rRNA reference in the gff file ...
written 6.0 years ago by
shl198 • 380
5
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... Hi all,
I aligned my RNA-seq against reference genome using tophat, I used the default aligner bowtie2.
And also the default parameters:
tophat -p 8 -G $annotation -o out $database L1_1.fq.gz L1_2.fq.gz
After got the results, I found out that in the unmapped.bam file, some reads have exact sam ...
written 6.0 years ago by
shl198 • 380
• updated
6.0 years ago by
Devon Ryan ♦ 95k
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For Is checking clustering of technical replicates necessary for RNAseq?
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