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updated 1 day ago by
Pierre Lindenbaum
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written 4 days ago by
Uveyik
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Recent Replies
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
GenoMax
145k
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
145k
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.
by
GenoMax
145k
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
by
GenoMax
145k
Please do not ask questions unrelated to the original post in this thread. Post a new question.
Comment: How to compile Multiz
by
Santex
•
0
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
•
0
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
•
0
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
•
0
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
•
0
oops
```
file *.out.bam
KO1_2Aligned.sortedByCoord.out.bam: gzip compressed data, extra field
KO1_2Aligned.toTranscriptome.out.bam: …
Answer: Converting bam to sam using htslib C++ api
by
Pierre Lindenbaum
164k
read https://github.com/samtools/samtools/blob/develop/sam_view.c
* allocate a new bam1_t* b = bam_init1
* open the input file: sam_op…
Comment: Converting bam to sam using htslib C++ api
by
Pierre Lindenbaum
164k
> 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…
Comment: FastQC and HISAT2
by
Jaber
•
0
Thank you, it worked almost after two months of struggle,
I nearly deleted everything and reinstalled it, I assume the problem was someth…
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