User: j.m.fustin

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j.m.fustin10
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j*********@pharm.kyoto-u.ac.jp

Posts by j.m.fustin

<prev • 14 results • page 1 of 2 • next >
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Answer: A: How to get counts for transcripts for all replicates
... Thank you for your answer. I am now joining the output tables from stringtie as you suggested! I was afraid that the lines of each sample table would be different but after **stringtie merge** on all transcript assemblies, then a second round of **stringtie** using the gtf output from **stringtie me ...
written 3 months ago by j.m.fustin10
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Answer: A: How to get counts for transcripts for all replicates
... Thanks Jen, but I believe this is not correct. Cufflinks will indeed generate a FPKM output for each input BAM file but then will generate a separate output file for each input, rather than one table containing all samples analyzed. Currently trying stringtie with stringmerge... JM ...
written 3 months ago by j.m.fustin10
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How to get counts for transcripts for all replicates
... Hi BIOSTARS, I have lots of samples that have been aligned to mm10 using RNA STAR. I have successfully assembled transcripts and merge the assembly for all samples using cufflinks. Although Cuffdiff has also worked I would to analyze data with a different statistical test that is not limited to pai ...
cuffdiff rna-seq fpkm cufflinks assembly written 3 months ago by j.m.fustin10
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Answer: A: --fr versus --rf option in Hisat2
... Hi Jen, Thanks a lot for your always useful comments. I thought it was so, but then I ran into a different problem. I first aligned with the option forward --fr, and got "70% reads aligned concordantly exactly 1 time". It seemed OK. Then, noticing my mistake with the library type, ran the same fast ...
written 3 months ago by j.m.fustin10
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--fr versus --rf option in Hisat2
... Hi! We have a library of paired reads generated by the UTF-8'en-us'SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian User Manual_063017 from Takara. Read1 is the antisense strand and Read2 is the sense. I wish to use Hisat2 for alignment but I am confused by two options: 1) Specify stra ...
rna-seq written 3 months ago by j.m.fustin10
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trimmomatic with paired-end
... Dear Biostar, I have paired-end sequencing data I would like to trim using trimmomatic. I have read 1 which matches the antisense sequence of the input and read 2 which is the sense paired-end read. I confirmed the presence of illumina adapter by fastQC. Can I simply use the provided Truseq3 (paire ...
trimmomatic galaxy adpator clip paired-end written 3 months ago by j.m.fustin10 • updated 3 months ago by Jennifer Hillman Jackson25k
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Answer: A: DiffBind on Galaxy
... Hi there, It was quite a while ago but if I remember well I "resolved" the problem by simply accessing Galaxy and generating my files with a PC (English OS) instead of my MacBook, and it worked. I hope it helps! JM ...
written 24 months ago by j.m.fustin10
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Tophat runs stay at the "This is a new dataset and not all of its data are available yet" for days.
... Hi There! I am experiencing some problems with Tophat. I have launched several analyses and it stays at the "This is a new dataset and not all of its data are available yet" stage without proceeding forward. It has now been one day without progress. I do not think there is a problem with my Fastq i ...
tophat written 2.3 years ago by j.m.fustin10 • updated 2.3 years ago by j.m.fustin270
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Answer: A: DiffBind on Galaxy
... ...and no, it does not. It is thus probably within the Galaxy system. ...
written 2.4 years ago by j.m.fustin10
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Answer: A: DiffBind on Galaxy
... Hi Zachary, Hi Jen, I believe the problem is in the automatic creation of the csv file describing the samples and contrasts for running DiffBind. This csv file should be encoded in "en_US.UTF-8" (as you can set up on a MAC) but apparently it is not, either because of the galaxy system or because of ...
written 2.4 years ago by j.m.fustin10

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Popular Question 24 months ago, created a question with more than 1,000 views. For DiffBind on Galaxy

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