0
votes
0
replies
42
views
0
votes
0
replies
40
views
3
votes
6
replies
405
views
1
vote
1
reply
154
views
updated 1 day ago by
Istvan Albert
101k
•
written 1 day ago by
Joe Kherery
▴
140
0
votes
0
replies
136
views
5
votes
9
replies
542
views
updated 2 days ago by
Shred
★
1.5k
•
written 4 days ago by
marionette.kent
•
0
1
vote
4
replies
304
views
1
vote
5
replies
354
views
2
votes
1
reply
237
views
0
votes
0
replies
163
views
0
votes
0
replies
163
views
10 days ago by
ZZOYEA
▴
20
0
votes
0
replies
172
views
1
vote
4
replies
577
views
updated 10 days ago by
Brian Bushnell
20k
•
written 21 days ago by
obsto123
•
0
0
votes
0
replies
122
views
0
votes
2
replies
686
views
1
vote
3
replies
333
views
3
votes
4
replies
343
views
11 days ago by
fifty_fifty
▴
70
12
votes
23
replies
15k
views
11 follow
updated 13 days ago by
Kimaya
•
0
•
written 5.3 years ago by
jared.andrews07
★
17k
1
vote
3
replies
317
views
0
votes
2
replies
251
views
updated 10 days ago by
Brian Bushnell
20k
•
written 20 days ago by
fluentin44
▴
20
1
vote
1
reply
280
views
0
votes
2
replies
339
views
updated 20 days ago by
Ram
44k
•
written 22 days ago by
ben.j.wendel
•
0
3
votes
1
reply
324
views
updated 22 days ago by
Radu Tanasa
▴
140
•
written 22 days ago by
pinheirofabiano
▴
90
1
vote
3
replies
396
views
updated 19 days ago by
Zhenyu Zhang
★
1.2k
•
written 24 days ago by
Znow
▴
20
2
votes
3
replies
381
views
updated 24 days ago by
dsull
★
6.8k
•
written 24 days ago by
karlensberg
•
0
1
vote
5
replies
402
views
0
votes
0
replies
199
views
0
votes
2
replies
271
views
6
votes
2
replies
4.9k
views
updated 25 days ago by
Assa Yeroslaviz
★
1.9k
•
written 6.2 years ago by
1769mkc
★
1.2k
0
votes
1
reply
208
views
0
votes
0
replies
168
views
1
vote
2
replies
397
views
12
votes
6
replies
838
views
4 weeks ago by
Matheus
•
0
4
votes
4
replies
483
views
5
votes
2
replies
282
views
updated 4 weeks ago by
Ram
44k
•
written 4 weeks ago by
Shicheng Guo
★
9.5k
1
vote
4
replies
404
views
0
votes
0
replies
145
views
4 weeks ago by
ZZOYEA
▴
20
0
votes
3
replies
331
views
1
vote
3
replies
293
views
0
votes
1
reply
272
views
updated 4 weeks ago by
james.hawley
▴
50
•
written 5 weeks ago by
jayeshkumarsundaram
•
0
5
votes
2
replies
303
views
updated 4 weeks ago by
Trivas
★
1.8k
•
written 4 weeks ago by
Joe Kherery
▴
140
1
vote
0
replies
155
views
updated 4 weeks ago by
Ram
44k
•
written 4 weeks ago by
Kat @ EdGe
▴
10
0
votes
4
replies
542
views
6 follow
updated 5 weeks ago by
Kevin Blighe
88k
•
written 7 weeks ago by
Esraa
•
0
0
votes
1
reply
342
views
0
votes
2
replies
336
views
updated 5 weeks ago by
Ram
44k
•
written 5 weeks ago by
alphaflylizard
•
0
2
votes
4
replies
454
views
0
votes
0
replies
167
views
0
votes
1
reply
193
views
updated 5 weeks ago by
Ram
44k
•
written 5 weeks ago by
drajangirija
•
0
1
vote
2
replies
283
views
5 weeks ago by
Aspire
▴
350
Recent Votes
Recent Locations •
All
Japan, 3 minutes ago
United States, 4 minutes ago
India, 7 minutes ago
Hong Kong, 9 minutes ago
India, 13 minutes ago
United States, 21 minutes ago
China, 24 minutes ago
Recent Awards •
All
Popular Question to
KatharinaKopp
•
0
Popular Question to
CRL-CHAR
•
0
Teacher to
tothepoint
▴
930
Popular Question to
bookorg
▴
10
Popular Question to
dpc
▴
250
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…
Traffic: 1304 users visited in the last hour
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by the
version 2.3.6
version 2.3.6