User: Kai_Qi

gravatar for Kai_Qi
Kai_Qi100
Reputation:
100
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Trusted
Location:
Chicago, IL
Last seen:
9 hours ago
Joined:
5 years, 7 months ago
Email:
q***********@gmail.com

Posts by Kai_Qi

<prev • 135 results • page 1 of 14 • next >
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Comment: C: Does .sra.cache file means failed download?
... I have also met with the same problem recently: some of the fastq file generate "SRR3532923.sra.cache", and I used `vdb-validate SRR3532923.sra.cache` to check it, which shows: 2020-09-17T20:04:18 vdb-validate.2.10.7 info: Table 'SRR3532923.sra.cache' metadata: md5 ok 2020-09-17T20:04:18 vd ...
written 10 days ago by Kai_Qi100
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Comment: C: Checking integrity of SRA downloaded fastq files
... Actually, when you download the fastq files in will generate sra file in a place where you set in the SRA toolkit. You can use vdb-validate to test. I used to delete them, but after the above mentioned discussion, I will use them first and them delete them. Hope it helps, Kai ...
written 11 days ago by Kai_Qi100
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Comment: C: DESeq2 results comparison
... Hi Kevin: How can I delete this one? It looks that there are too many questions and too long. Maybe delete it is an option? ...
written 5 weeks ago by Kai_Qi100
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Comment: C: sbacth on multiple fastq files sequentially
... Many thanks for comprehensive solutions! ...
written 5 weeks ago by Kai_Qi100
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Comment: C: sbacth on multiple fastq files sequentially
... I just checked the running progress. It worked well. one question is that the starmapping_sbatch_error and starmapping_sbatch_out was overwrote. Is there a way to keep it for individual fastq? ...
written 5 weeks ago by Kai_Qi100
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Comment: C: sbacth on multiple fastq files sequentially
... Thanks a lot for your comments. I am going to revise it back. ...
written 5 weeks ago by Kai_Qi100
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Comment: C: sbacth on multiple fastq files sequentially
... For your comments: "Note: You are asking for 16 threads on your STAR command line but requesting only 10 tasks per node (and 1 node) on SLURM side. You should match those two numbers, either up or down". I have been using this for a while, will this cause problem for downstream analysis? Thanks ag ...
written 5 weeks ago by Kai_Qi100
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Comment: C: sbacth on multiple fastq files sequentially
... Thanks! I will put the for loop in "loop_script.sh" file and do bash. I will be back to update how it works ...
written 5 weeks ago by Kai_Qi100
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sbacth on multiple fastq files sequentially
... I have an file named "starmapping.sh" which I used for mapping fastq files using STAR. My use is : sbatch strarmapping.sh SRR123456 I have been used it to map individual fastq files for a while. Currently, I have 10 fastq, if I wait for one submitted job finished and then submit another one it ...
alignment star rna-seq written 5 weeks ago by Kai_Qi100
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Comment: C: difficulties in merge multiple txt files from Rsubread feature counts to DESEQ2
... Thank you! I see the results, it is exactly as you said. ...
written 6 weeks ago by Kai_Qi100

Latest awards to Kai_Qi

Centurion 3 months ago, created 100 posts.
Supporter 4 months ago, voted at least 25 times.

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