User: corend

gravatar for corend
corend20
Reputation:
20
Status:
New User
Location:
Last seen:
an hour ago
Joined:
3 months, 3 weeks ago
Email:
c***************@gmail.com

Posts by corend

<prev • 14 results • page 1 of 2 • next >
0
votes
0
answers
108
views
0
answers
Comment: C: Why does cufflinks split this transcript?
... Nope, they overlap very well (not worse than any other junctions). I changed all parameters one by one, I always get this transcript split in2. The only way to have it full is to use faux-reads from a guide annotation (and I don't want to use a guide annotation). ...
written 19 hours ago by corend20
0
votes
0
answers
108
views
0
answers
Comment: C: Why does cufflinks split this transcript?
... I just filtered out multimapped reads, and I have 67 reads supporting the junction instead of 77. It seems that this is not a multimapping problem :/ ...
written 1 day ago by corend20
4
votes
0
answers
108
views
0
answers
Why does cufflinks split this transcript?
... I have a RNA-seq dataset. I used `Tophat` and `Cufflinks` to align to my reference genome and make an assembly of my transcripts driven by a `GTF` of my genome. I have an interest gene (9 exons), I am looking if it is expressed in my data. When I look at it in the assembly, I found it split in 2 pa ...
assembly cufflinks rna-seq written 5 days ago by corend20
3
votes
1
answer
146
views
1
answer
What is an "unanchored contig"?
... What is the difference between and anchored and an unanchored contig? I found informations saying that chromosome location is known for anchored contigs, but does it mean that contig1 = chr1, or that contig1 = somewhere on chromosome 1? > An anchored scaffold or contig is one whose location on ...
assembly sequencing written 29 days ago by corend20 • updated 28 days ago by h.mon10k
0
votes
1
answer
187
views
1
answers
Comment: C: How to get an XS field in SAM with unstranded data ?
... Thanks a lot, I'll try this option, I see that there is also a `dta-cufflinks` option. I could be what I am looking for. Still, I don't understand why does `cufflinks` requires a strandness information, when I don't have the strand information in my data. Also, we if I use `lib-type unstranded`, wh ...
written 6 weeks ago by corend20
0
votes
1
answer
187
views
1
answers
Comment: C: How to get an XS field in SAM with unstranded data ?
... I used Hisat2 for the unstranded alignment ...
written 6 weeks ago by corend20
0
votes
1
answer
187
views
1
answers
Comment: C: How to get an XS file in SAM with unstranded data ?
... That was helpful, thanks, I just edited my post ...
written 6 weeks ago by corend20
4
votes
1
answer
187
views
1
answer
How to get an XS field in SAM with unstranded data ?
... *Initial post title : How does cufflinks find the strand of a novel transcript?* I am using `cufflinks` to create a RABT assembly of a genome. I have my newly created `merged.gtf` file. Most of new transcripts found by `cufflinks` are present on both strands. I mean that very close transcripts (i ...
cufflinks alignment rna-seq written 6 weeks ago by corend20 • updated 6 weeks ago by Friederike920
0
votes
2
answers
224
views
2
answers
Comment: C: DESeq2 biais when genes are missing from the annotation?
... I don't know what is the proportion of rRNA in my data, but the sequencing what made purifying polyA RNAs. As you and the previous answer suggested, I will build a new gff with cufflinks, it seems to be the best option ! ...
written 9 weeks ago by corend20
0
votes
2
answers
224
views
2
answers
Comment: C: DESeq2 biais when genes are missing from the annotation?
... My expression levels are supposed to be similar as I work on different tissues of the same organism. But building a new gff with cufflinks and use it to improve my results seems a good option ! ...
written 9 weeks ago by corend20

Latest awards to corend

Supporter 26 days ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1269 users visited in the last hour