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Forum: Events / Conferences 01-18-2018, 05:28 AM
Replies: 0
Views: 2,557
Posted By super0925
Lightbulb 4th Annual Viral Genomics & Bioinformatics Training Course (20-24 August 2018)

The MRC-University of Glasgow Centre for Virus Research (CVR) has been running a successful training course on Viral Bioinformatics and Genomics annually since 2015 and applications are now open for...
Forum: RNA Sequencing 09-06-2016, 02:02 PM
Replies: 0
Views: 1,252
Posted By super0925
how many reads per sample would you recommend in single cell RNA-Seq (e.g. Cel-Seq)

Has anybody done single cell RNA-Seq especially Cel-Seq before?
How many reads per samples would you recommend? I know standard RNA-Seq could better has ~30M per sample and > 3 samples per...
Forum: Sample Prep / Library Generation 09-06-2016, 01:57 PM
Replies: 1
Views: 1,360
Posted By super0925
The number of reads of each sample in single cell RNA-Seq

Has anybody done single cell RNA-Seq especially Cel-Seq before?
How many reads per samples would you recommend? I know standard RNA-Seq could better has ~30M per sample and > 3 samples per...
Forum: Bioinformatics 05-30-2016, 11:13 PM
Replies: 6
Views: 3,885
Posted By super0925
Hi I have same problem. It seems that lots of...

Hi I have same problem. It seems that lots of people have this error.

I use the Ensembl genome(*dna.toplevel.fa) and GTF file.

If I ran cufflinks (even without -b genome.fa) but then run...
Forum: Bioinformatics 04-30-2016, 10:16 AM
Replies: 7
Views: 1,883
Posted By super0925
Hi D I tried it, but still get the error. ...

Hi D
I tried it, but still get the error.
"Error occured when processing SAM input (line 4240949 of file aligned.sam):
("Malformed SAM line: RNAME == '*' although flag bit &0x0004 cleared",...
Forum: Bioinformatics 04-29-2016, 07:13 AM
Replies: 7
Views: 1,883
Posted By super0925
Sorry I got SAME error!! I re-run the tophat,...

Sorry I got SAME error!!
I re-run the tophat, get the accepted_hits.bam , command is as follows:


tophat2 -o outdir --library-type fr-firststrand --keep-fasta-order --GTF genes.gtf genome.fa...
Forum: Bioinformatics 04-29-2016, 03:51 AM
Replies: 7
Views: 1,883
Posted By super0925
OK. I will try re-run it. I use tophat2 -o...

OK. I will try re-run it.
I use
tophat2 -o outdir --library-type fr-firststrand --keep-fasta-order --GTF genes.gtf genome.fa Trimmed.fastq
and get the aligned.bam, which I don't think there...
Forum: Bioinformatics 04-29-2016, 03:39 AM
Replies: 7
Views: 1,883
Posted By super0925
1.Do you mean I need to re-map the sample? 2....

1.Do you mean I need to re-map the sample?
2. Doe it mean that My cuffdiff could also potentially have problem?
I ran 6 samples in a loop (Mapping, sorting BAM, Counting Reads)and hence I think the...
Forum: Bioinformatics 04-29-2016, 03:01 AM
Replies: 7
Views: 1,883
Posted By super0925
htseq-count error RNAME == '*' although flag bit &0x0004 cleared"

Hi all

I do rna-seq , after tophat mapping, I got 6 aligned.bam file . And I played them by Cuffdiff, it works. However, if I try Htseq-count on 6 aligned.bam file (I have sorted and transfer it...
Forum: Bioinformatics 03-18-2016, 02:39 AM
Replies: 5
Views: 1,305
Posted By super0925
Hi Brian Thank you so much! 1. I always keep...

Hi Brian
Thank you so much!
1. I always keep reads>20bp in Illumina. I am doing mRNA-Seq.
But do you mean if ncRNA, I need to keep <20bp if the Quality score >28.
2. The staff who do the...
Forum: Bioinformatics 03-17-2016, 08:31 AM
Replies: 5
Views: 1,305
Posted By super0925
(1) How about reads length <20bp , I have trimmed...

(1) How about reads length <20bp , I have trimmed them. Does it impact results too much? I thought your suggestion is better to leave them.

(2) And besides general adapter, if fastqc shows...
Forum: RNA Sequencing 01-18-2016, 02:43 AM
Replies: 4
Views: 1,150
Posted By super0925
Yep. I think maybe we need call it 'Anonymous...

Yep. I think maybe we need call it 'Anonymous gene' to explain 'the gene without annotation at the genome '
Forum: Bioinformatics 01-15-2016, 05:11 AM
Replies: 1
Views: 1,315
Posted By super0925
RNA-Seq: GFOLD counts is different from HTSeq-count

Does anybody use GFOLD before?
http://compbio.tongji.edu.cn/~fengjx/GFOLD/gfold.html

Why do I use these two tools count reads but give different results?

In GFOLD manual, “Because of possible...
Forum: Bioinformatics 01-13-2016, 05:04 AM
Replies: 7
Views: 2,646
Posted By super0925
Done! Thx!

Done! Thx!
Forum: Bioinformatics 01-13-2016, 02:00 AM
Replies: 7
Views: 2,646
Posted By super0925
Brilliant you are! I will try it ! PS: So...

Brilliant you are! I will try it !

PS: So do I need to add those UTR, CDS, transcript, etc? I don't think so. I only want to look at differential gene expression of this pseudo gene (I am sure...
Forum: Bioinformatics 01-12-2016, 08:31 AM
Replies: 7
Views: 2,646
Posted By super0925
I remember I have added not only exon but also...

I remember I have added not only exon but also UTR, but I failed. So I only keep the exon and post this thread.
I tried your command

$ head --lines=2 henan.gtf | od -c
0000000 2 9 ...
Forum: RNA Sequencing 01-12-2016, 02:18 AM
Replies: 4
Views: 1,150
Posted By super0925
how to look at differential expression of a pseduo gene?

Hi all

When do RNA-Seq analysis, after I have finished the alignment by Tophat and get the accpeted_hits.bam. Now I want to looked at if it is has differential expression at the corresponding...
Forum: Bioinformatics 01-12-2016, 02:05 AM
Replies: 7
Views: 2,646
Posted By super0925
how to add a pseduo gene into a GTF file?

Hi all

When do RNA-Seq analysis, after I have finished the alignment by Tophat and get the accpeted_hits.bam. Now I want to looked at if it is has differential expression at the corresponding...
Forum: Bioinformatics 09-14-2015, 06:26 AM
Replies: 22
Views: 18,784
Posted By super0925
Thank you D. Very helpful. And I also found...

Thank you D. Very helpful.
And I also found Cufflinks could calculate RPKM directly.
by
cufflinks -o OutDir -g hg19/genes.gtf TopHat/accepted_hits.bam
Forum: Bioinformatics 09-11-2015, 06:23 AM
Replies: 22
Views: 18,784
Posted By super0925
Hi D Brilliant! It works. I have just...

Hi D
Brilliant! It works.
I have just changed one command
GTF <- import.gff(GTFfile, format="gtf", genome="hg19", asRangedData=F, feature.type="exon")
However, the result only contain 25369...
Forum: Bioinformatics 09-10-2015, 08:30 PM
Replies: 22
Views: 18,784
Posted By super0925
Sorry D, I didn't totally get what you said. ...

Sorry D, I didn't totally get what you said.
The genes.gtf and genome.fa are downloaded from the latest UCSC homo sapiens hg19 genome.
How could I 'download the matching fasta' or 'remove the...
Forum: Bioinformatics 09-10-2015, 08:52 AM
Replies: 22
Views: 18,784
Posted By super0925
Hi a_mt Could you give me the commands? I don't...

Hi a_mt Could you give me the commands? I don't know how to transfer from SAM to wiggle by bedtools.
I now have sample.BAM , genome.fa and genes.gtf in the same directory.
Thank you very much!
Forum: Bioinformatics 09-10-2015, 08:32 AM
Replies: 22
Views: 18,784
Posted By super0925
Hi D I found your post to calculate the gene...

Hi D

I found your post to calculate the gene length.
I have one BAM file and want to get the RPKM for each genes. I have the genes.gtf and genome.fa in the same directory.
For your script, I...
Forum: Bioinformatics 08-05-2015, 06:54 AM
Replies: 6
Views: 1,313
Posted By super0925
I want to ouput XML (option 5), so...

I want to ouput XML (option 5),
so either"-max_target_seqs" or " -num_descriptions and -num_alignments" works???
Forum: Bioinformatics 08-05-2015, 06:14 AM
Replies: 6
Views: 1,313
Posted By super0925
I got it. It is -max_target_seqs 5 Thank you

I got it.
It is -max_target_seqs 5
Thank you
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