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Recent Replies
Comment: How to compile Multiz
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Pierre Lindenbaum
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> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
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I solved the problem by installing `NMF` package.
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
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Can you check using `featureCounts` to make sure things look reasonable with alignments? You could also use `salmon` to do transcript quant…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
GenoMax
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Since we don't have access to your data we can't comment. Check the integrity of your input data files. Validate the files if you are not s…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
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GenoMax
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https://www.biostars.org/u/145859/ : Use `ADD REPLY/ADD COMMENT` to add additional information to existing threads. `ADD YOUR ANSWER` is me…
Comment: How to compile Multiz
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Please do not ask questions unrelated to the original post in this thread. Post a new question.
Comment: How to compile Multiz
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Santex
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I could install multiz from it! Thank you very much. Please help me out with the problem below.
I run multiz like below.
(myenv) tak…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
•
0
One of them looks okay, but I don't quite believe it.
```R
> table(df$`intermediate_data.OE1_1_.genes.results`==0)
FALSE TRUE
21200 2…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
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It seems that the files that generated the results also have significant issues. Except for one sample, all other samples only have over 20…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
•
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Their .fq files all look similar, should I rerun these programs?
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
GenoMax
145k
> Cannot open intermediate_data/OE_NC_2_.temp/OE_NC_2__alignable_1.fq! It may not exist.
Looks like you are missing some files.
BTW this …
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
•
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The most torturous thing is that some groups did indeed generate results.
```
ls intermediate_data
KO1_1_.stat KO1_3_.isoforms…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
•
0
However, OE1_2 and OE1_3 are not the only groups experiencing problems. I tried another non-empty file, and:
```
rsem-calculate-expression …
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
•
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oops
```
file *.out.bam
KO1_2Aligned.sortedByCoord.out.bam: gzip compressed data, extra field
KO1_2Aligned.toTranscriptome.out.bam: …
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