0
votes
0
replies
11
views
0
votes
2
replies
79
views
updated 4 hours ago by
Pierre Lindenbaum
164k
•
written 5 hours ago by
Uveyik
▴
20
0
votes
0
replies
38
views
0
votes
0
replies
36
views
819
votes
169
replies
155k
views
110 follow
updated 11 days ago by
Biostar
3.0k
•
written 7.8 years ago by
Istvan Albert
101k
0
votes
0
replies
45
views
0
votes
6
replies
132
views
23 minutes ago by
Pallondyle
•
0
1
vote
1
reply
72
views
updated 9 hours ago by
Pierre Lindenbaum
164k
•
written 9 hours ago by
ChumBucket2024
•
0
3
votes
6
replies
397
views
0
votes
0
replies
54
views
1
vote
1
reply
106
views
updated 11 hours ago by
Pierre Lindenbaum
164k
•
written 12 hours ago by
Santex
•
0
0
votes
0
replies
49
views
15 hours ago by
carlopecoraro2
★
2.6k
0
votes
2
replies
146
views
0
votes
3
replies
349
views
0
votes
2
replies
120
views
18 hours ago by
SEJAL
•
0
3
votes
2
replies
144
views
0
votes
0
replies
90
views
0
votes
0
replies
68
views
1 day ago by
saamhasan55
▴
10
0
votes
0
replies
94
views
0
votes
5
replies
351
views
0
votes
0
replies
89
views
1 day ago by
SEJAL
•
0
0
votes
0
replies
82
views
3
votes
4
replies
226
views
1
vote
6
replies
431
views
updated 1 day ago by
colindaven
6.7k
•
written 2 days ago by
Jyoti
•
0
1
vote
1
reply
151
views
updated 1 day ago by
Istvan Albert
101k
•
written 1 day ago by
Joe Kherery
▴
140
0
votes
2
replies
258
views
updated 1 day ago by
Istvan Albert
101k
•
written 2 days ago by
pinheirofabiano
▴
90
0
votes
2
replies
252
views
4
votes
2
replies
317
views
4
votes
1
reply
152
views
updated 1 day ago by
Pierre Lindenbaum
164k
•
written 1 day ago by
Uveyik
▴
20
0
votes
0
replies
140
views
0
votes
1
reply
187
views
updated 2 days ago by
bk11
★
2.9k
•
written 2 days ago by
Varun Gupta
★
1.3k
0
votes
0
replies
128
views
0
votes
4
replies
381
views
5
votes
2
replies
236
views
0
votes
0
replies
134
views
2
votes
1
reply
178
views
5
votes
9
replies
540
views
updated 2 days ago by
Shred
★
1.5k
•
written 4 days ago by
marionette.kent
•
0
0
votes
0
replies
128
views
2 days ago by
myoui3122010
▴
20
5
votes
12
replies
8.0k
views
updated 2 days ago by
GenoMax
145k
•
written 5.6 years ago by
marongiu.luigi
▴
710
1
vote
0
replies
135
views
2 days ago by
carlopecoraro2
★
2.6k
0
votes
1
reply
523
views
updated 2 days ago by
Volter
•
0
•
written 15 months ago by
jaredgichohi
•
0
23
votes
11
replies
602
views
7 follow
1
vote
1
reply
307
views
2
votes
4
replies
1.6k
views
updated 2 days ago by
jayeshkumarsundaram
•
0
•
written 3.3 years ago by
thomas.welch
▴
50
0
votes
0
replies
145
views
7
votes
5
replies
436
views
updated 2 days ago by
Gordon Smyth
★
7.4k
•
written 4 days ago by
Haad
•
0
0
votes
0
replies
147
views
3 days ago by
sooni
▴
20
0
votes
2
replies
255
views
2 days ago by
ChumBucket2024
•
0
Recent Votes
Recent Locations •
All
United States, just now
China, 6 minutes ago
Hong Kong, 6 minutes ago
United States, 10 minutes ago
Saudi Arabia, 21 minutes ago
United States, 22 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
Teacher to
Pierre Lindenbaum
164k
Recent Replies
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…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pierre Lindenbaum
164k
what is the output of
```
file *.out.bam
```
?
Answer: MarkDuplicatesSpark GATK flags for overcoming space issues
by
Pierre Lindenbaum
164k
https://gatk.broadinstitute.org/hc/en-us/articles/360037224932-MarkDuplicatesSpark
> Furthermore, we recommend explicitly setting the Sp…
Comment: FastQC and HISAT2
by
GenoMax
145k
You seem to have done the right steps (and I assume you are familiar with `$PATH` and concept of relative paths). Do you also have `java` i…
Comment: FastQC and HISAT2
by
Jaber
•
0
Thank you,
Yes I use linux on windows, I installed perl, the option to choose which software I want to open the file with have not disappe…
Comment: How to compile Multiz
by
Pierre Lindenbaum
164k
how about using bioconda to install this software ? https://bioconda.github.io/recipes/multiz/README.html
Comment: Can't run CrossMap
by
Muhammad
•
0
it produces
/home/myname/micromamba/envs/bioinfo/bin/python3
tried to do
conda create --name bioinfo python=3.y -y
but when i …
Comment: ncRNA, pseudogenes and lncRNA genes in highly variable features ( scRNA)
by
dsull
★
6.8k
Remove genes. After all, it’s those genes that are problematic.
Traffic: 1295 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