User: joomi

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joomi0
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Posts by joomi

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Alternative Splicing detection and tools (Kallisto, sleuth, isoformSwitchAnalyze
... Hello again, I was wondering if I could ask about this error: Step 1 of 6: Checking data... Step 2 of 6: Obtaining annotation... importing GTF (this may take a while) Step 3 of 6: Calculating gene expression and isoform fraction... 632 ( 0.85%) isoforms were removed since they were not ...
written 8 days ago by joomi0
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Alternative Splicing detection and tools (Kallisto, sleuth, isoformSwitchAnalyzeR)
... Hello, I hope this actually leads to a few answers, but I have RNASeq data and I want to study alternative splicing/isoform switch between two conditions. I'm not sure what tools to use, but I have done transcript quantification with Kallisto. The results are on a cluster and overall we have 672 ...
R rna-seq written 12 days ago by joomi0 • updated 10 days ago by kristoffer.vittingseerup3.3k
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Comment: C: Alternative splicing analysis following kallisto?
... Hey Dina.hesham139 can I ask you what you ended up using? I'm using Kallisto also and Sleuth, but then someone mentioned that Sleuth might not be the best method. I was wondering what you used? ...
written 12 days ago by joomi0
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Comment: C: Tools To Do the Alternative Splicing Analysis
... Thank you so much for this! You are an angel! One question, how do we import our data into R if we do transcript quantification on a cluster? The resulting transcript quantification is very large and can't be imported outside of the cluster and R analysis is much easier outside of a cluster. ...
written 12 days ago by joomi0
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Comment: A: diffSplice: Error in exon.genes[o, , drop = FALSE] : incorrect number of dimensi
... Was this solved, I have a similar issue? ...
written 12 months ago by joomi0
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Comment: C: bwa is getting stuck
... Thank you so much! I subsetted the two reads with zcat and ran bwa. It completed within minutes! My original files are around 7.4G in size and contain around 21959218 reads. This is for the species Zea Mays and in all of my runs I have used around 60G which is 64G/63g is the maximum that I have acce ...
written 19 months ago by joomi0
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Comment: C: bwa is getting stuck
... Hello, I don't have a log file. I have an standard output file and standard error file. The standard output looks like this: ========================================== SLURM_JOB_ID = 7116608 SLURM_NODELIST = c9-68 ========================================== and the standard error ...
written 19 months ago by joomi0
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Comment: C: bwa is getting stuck
... Hello, I should have mentioned that I already redirect to a sam file! Sorry about that. My main issue is that all my scripts are timing out. I've been running them for 24 hours and they end up stuck at the point in the standard error files. I'm not sure why it is so slow. Is this normal? How many d ...
written 19 months ago by joomi0
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Comment: A: bwa is getting stuck
... Hello, I should have mentioned that I already redirect to a sam file! Sorry about that. My main issue is that all my scripts are timing out. I've been running them for 24 hours and they end up stuck at the point in the standard error files. I'm not sure why it is so slow. Is this normal? How many ...
written 19 months ago by joomi0
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bwa is getting stuck
... Hello, I've been running bwa mem to do pair wise alignment to a reference. I have already indexed my reference and it resulted in 5 output files with the following extensions: .pac, .sa, .amb, .ann, .bwt. I have run bwa men with 60G multiple times now and all the jobs never finish. They take over ...
mem alignment bwa rna-seq written 19 months ago by joomi0

Latest awards to joomi

Popular Question 12 months ago, created a question with more than 1,000 views. For How do I filter my VCF file to only include certain coordinates from a BED file?
Popular Question 12 months ago, created a question with more than 1,000 views. For VCFtools --exclude-bed Does it include from the BED file or exclude only?

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