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Search: Posts Made By: gcR
Forum: Bioinformatics 11-30-2020, 05:59 AM
Replies: 1
Views: 881
Posted By gcR
I got this answer from another forum, so I add it...

I got this answer from another forum, so I add it here in case someone needs it.

input:

output:
Forum: Bioinformatics 11-11-2020, 08:37 AM
Replies: 1
Views: 881
Posted By gcR
How can I extract each APAsite possibility from this table?

Hello,

I have an output from APATrap package, which gives back the predicted APA sites from samples. I need to make a list from all the possibles APAs to cross it with miRNAs database and get...
Forum: Bioinformatics 05-05-2017, 11:08 AM
Replies: 1
Views: 1,733
Posted By gcR
featureCounts exon-level, problems with the counting verification

Hey, I was asked to do some analysis at exon level with featureCounts from a sample of stem cells induced to adypocites, and this was my result:
fc5 <- featureCounts(filevar, annot.ext =...
Forum: Bioinformatics 04-12-2017, 11:10 AM
Replies: 16
Views: 6,343
Posted By gcR
Found the drama, the BAM files were corrupt, had...

Found the drama, the BAM files were corrupt, had to DL the dataset again and problem solved.

Dummy begginers problems, indeed :(

Thx for ur time.
Forum: Bioinformatics 04-12-2017, 10:53 AM
Replies: 16
Views: 6,343
Posted By gcR
You were right, I had been working on that and...

You were right, I had been working on that and fixed it alredy. Thanks.

Now, the featureCounts function says my files are .SAM, altought even checking on bash the class type its .BAM

It seems...
Forum: Bioinformatics 04-11-2017, 12:31 PM
Replies: 16
Views: 6,343
Posted By gcR
Yes, it is hahah. Thanks for your help. ...

Yes, it is hahah. Thanks for your help.

annotation.gtf already formated:
$ head -4 data3filtrada3
1 havana exon 11869 12227 "ENSE00002234944"; "DDX11L1"; "processed_transcript";...
Forum: Bioinformatics 04-11-2017, 11:12 AM
Replies: 16
Views: 6,343
Posted By gcR
I think so, I have already worked with some files...

I think so, I have already worked with some files from these people and had no problems, this would be a 2nd experiment.

I tried to install Rsamtools and Rbamtools without success, tried from bash...
Forum: Bioinformatics 04-11-2017, 09:48 AM
Replies: 16
Views: 6,343
Posted By gcR
Finally, I changed my RSubread version to 1.14.0...

Finally, I changed my RSubread version to 1.14.0 and worked indeed.

Still having some problems, but at least Im progressing and understanding.

Now it says my annotationfile.gtf is SAF, so I...
Forum: Bioinformatics 04-11-2017, 08:29 AM
Replies: 16
Views: 6,343
Posted By gcR
Sorry for my late response, I had been checking...

Sorry for my late response, I had been checking other things about it.

Apparently the annotation.gtf has no problems, since I changed the annotation to an inbuilt one and had the same error.
...
Forum: Bioinformatics 04-11-2017, 06:21 AM
Replies: 16
Views: 6,343
Posted By gcR
Again, tried with: ./featureCounts -t...

Again, tried with:



./featureCounts -t exon -g gene_id -a data2.gtf -o counts.txt ./4_GCCAAT_L001_R1_001.bam




./featureCounts -t exon -g gene_id -a data2.gtf -o counts.txt...
Forum: Bioinformatics 04-11-2017, 05:46 AM
Replies: 16
Views: 6,343
Posted By gcR
[sysadm@sysadm bin]$ ./featureCounts -t exon -g...

[sysadm@sysadm bin]$ ./featureCounts -t exon -g gene_id -a data2.gtf -o counts.txt 4_GCCAAT_L001_R1_001.bam 8_AGTTCC_L001_R1_001.bam 16_GCCAAT_L002_R1_001.bam 20_AGTTCC_L003_R1_001.bam...
Forum: Bioinformatics 04-11-2017, 04:06 AM
Replies: 16
Views: 6,343
Posted By gcR
Thanks for your fast response. In fact I...

Thanks for your fast response.

In fact I didn't, I copy-pasted the code format from Wei Shi examples, but my filenames are different.

I think the problem is in the path, but although I give...
Forum: Bioinformatics 04-10-2017, 12:59 PM
Replies: 16
Views: 6,343
Posted By gcR
RSubread: featureCounts problem with input .bam files

Hello, I have been having an issue with this function featureCounts() for reads summarize.

I want to make an analysis from exons. Everything worked fine until now, but seems like I cant give the...
Forum: Bioinformatics 04-03-2017, 05:24 PM
Replies: 3
Views: 2,750
Posted By gcR
Thanks you so much, sry for my late answer, I had...

Thanks you so much, sry for my late answer, I had some personal issues to attend but I got your answer immediatly and was much helpful.

G.
Forum: Bioinformatics 03-29-2017, 12:24 PM
Replies: 3
Views: 2,750
Posted By gcR
Looking for GTF file of exon annotations (GRCh38/hg38) without success

Hello, Im new to the site and to be honest, to bioinformatics.

I will sum it up, im having problems finding the correct file, although I passed the evening checking the forum, github, and other...
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