User: kamoltip.lao

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Posts by kamoltip.lao

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Something strange in RNA-seq raw reads, It is contamination or not?
... It will be better if I perform sequencing for both conditions in the same batch, right? Just in case, I cannot collect more sample to run as replicate, only 1 sample for each condition, is it enough? I have a limitation with my sample, it's very difficult to collect. So, I could prepare only 2 repl ...
written 4 months ago by kamoltip.lao0
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Comment: C: Something strange in RNA-seq raw reads, It is contamination or not?
... I already contacted them but they said this issue is not contamination but they cannot explain why. ...
written 4 months ago by kamoltip.lao0
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Comment: C: Something strange in RNA-seq raw reads, It is contamination or not?
... I'll perform the PCA to see the pattern as your suggestion. I planned to prepare a new sample B, so It will be better if I know the possible reason that I can avoid next time. Thank you so much ...
written 4 months ago by kamoltip.lao0
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Comment: C: Something strange in RNA-seq raw reads, It is contamination or not?
... Yes, when I looked at 47% of reads that matched to my model, some reads are matched to ribosomal genes. The rest with 'No hit' status, I also found ribosomal genes of other organisms but just 20 -70 bp in the middle of 101 bp reads are matched. Have you ever experienced any issue like this? Than ...
written 4 months ago by kamoltip.lao0
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Comment: C: Something strange in RNA-seq raw reads, It is contamination or not?
... Thank you for your suggestion, I have checked the pre-library RNA QC and library QC reports but the quality of B2 is similar to other samples with RIN is 10. I prepared total RNA and sent it to the sequencing company to perform library preparation and sequencing for me. Is it possible that something ...
written 4 months ago by kamoltip.lao0
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Something strange in RNA-seq raw reads, It is contamination or not?
... Hi all, I'm a beginner for RNA-seq and bioinformatics. I found something strange in my RNA-seq raw read from an insect. I have 4 samples; A1, A2, B1, B2. Sample A1 - A2, and B1 - B2 are biological replicates. After I ran FastQC to qualify the quality of the raw reads. I got the warning from 'overr ...
rna-seq written 4 months ago by kamoltip.lao0 • updated 4 months ago by shawn.w.foley1.0k
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Comment: C: How can I view and manage the Trinity.fasta by bash
... Thank you so much, I got it. ...
written 8 months ago by kamoltip.lao0
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How can I view and manage the Trinity.fasta by bash
... Hi everyone, I'm a beginner and learning to analyze the sequence by practicing. Please give me a suggestion, How can I view and manage the assembly transcriptome from Trinity as Trinity.fasta by bash? $ less Trinity.fasta >TRINITY_DN30765_c0_g1_i1 len=228 path=[0:0-227] TGGCGAAGTT ...
rna-seq written 8 months ago by kamoltip.lao0 • updated 8 months ago by lieven.sterck5.8k
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Comment: C: Problem with fastq file
... You're right, I use macOS 10.14.2. After I installed GNU coreutils, I can use `gzcat test.fastq.gz | head` without any error. Thank you so much for kind help ...
written 9 months ago by kamoltip.lao0
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Answer: A: Problem with fastq file
... Dear all, Thank you so much for suggestions from everyone, I tried them all and I would like to inform everyone about my result. For `$ zcat test.fastq.gz | head` it does not function in my case. It always shows the error. `zcat: can't stat: test.fastq.gz (test.fastq.gz.Z): No such file or direct ...
written 9 months ago by kamoltip.lao0

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Scholar 9 months ago, created an answer that has been accepted. For A: Problem with fastq file

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