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Forum: Illumina/Solexa 02-20-2018, 03:28 AM
Replies: 0
Views: 753
Posted By bvk
Interpretation of Gene coverage profile from qualimap

Hi,

I see that qualimap bamqc and rnaseq shows us the coverage of genome and gene coverage profile (total). I would be very grateful if someone could take a quick look at these results and tell me...
Forum: RNA Sequencing 02-01-2018, 08:51 AM
Replies: 0
Views: 1,431
Posted By bvk
Hisat2 index with splice sites

Hello,

I would like to detect lncRNAs from RNA-seq data. Initially, I'm using Hisat2 for aligning the samples. For this I downloaded the human genome hisat2 index "genome_snp_tran" from the hisat2...
Forum: RNA Sequencing 12-31-2017, 12:30 AM
Replies: 16
Views: 4,276
Posted By bvk
Hello Kranti, Please check the above...

Hello Kranti,

Please check the above comment. That is what I got when I used the command you gave.
Forum: RNA Sequencing 12-29-2017, 03:55 AM
Replies: 16
Views: 4,276
Posted By bvk
Hello Kranti, May I know the answer for the...

Hello Kranti,

May I know the answer for the above comment.
Forum: RNA Sequencing 12-28-2017, 08:27 AM
Replies: 16
Views: 4,276
Posted By bvk
Like you said before I gave the command. And I...

Like you said before I gave the command. And I have an error now.

perl lncRNApipe --cpu 12 --run /path/lncRNApipe_28_12_2017_run1 --cat-ncRNAs "--extract-pat 'i|o|u|x|e' --ignore-genePred-err...
Forum: RNA Sequencing 12-28-2017, 07:39 AM
Replies: 16
Views: 4,276
Posted By bvk
Yes, I just got that from Ensembl site. And...

Yes, I just got that from Ensembl site. And running the commnad with that file. I will tell you if there are any errors.

BTW, could you please tell in which file output file from gffcompare I can...
Forum: RNA Sequencing 12-28-2017, 06:18 AM
Replies: 16
Views: 4,276
Posted By bvk
Hello Karthik, Could you please tell me what...

Hello Karthik,

Could you please tell me what I should do if I dont have .fa reference file. As I see in the hisat2 manual that there wont be any .fa files. Thank you
Forum: RNA Sequencing 12-28-2017, 05:45 AM
Replies: 16
Views: 4,276
Posted By bvk
No, I dont have any genome file in fasta format....

No, I dont have any genome file in fasta format. The reference genome I used for Hisat is from [https://ccb.jhu.edu/software/hisat2/manual.shtml] H.Sapiens GRCh37 (genome_snp_tran).

What I should...
Forum: RNA Sequencing 12-28-2017, 03:07 AM
Replies: 16
Views: 4,276
Posted By bvk
Hello, Need your help The output from...

Hello,

Need your help

The output from Stringtie-merge is "stringtie_merged.gtf" (6 samples). As you said I ran gffcompare command on output given by stringtie-merge.

gffcompare -r...
Forum: RNA Sequencing 12-11-2017, 05:27 AM
Replies: 16
Views: 4,276
Posted By bvk
Hello, I'm looking for detecting known and...

Hello,

I'm looking for detecting known and novel lncRNAs from RNA-Seq data. I have used HISAt2 for alignment and Stringtie for Transcript assembly as mentioned in this paper...
Forum: Ion Torrent 12-06-2017, 09:54 AM
Replies: 8
Views: 2,084
Posted By bvk
Ok. Differences between platforms is found here...

Ok. Differences between platforms is found here (https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4011-0).

Thank you
Forum: Ion Torrent 12-06-2017, 12:19 AM
Replies: 8
Views: 2,084
Posted By bvk
Yes it is Ion Torrent Amplicon Sequencing...

Yes it is Ion Torrent Amplicon Sequencing RNA-Seq. I see that TMAP is the best alignment tool for this data. I would like to know how to do the quantification and how to get the gene-level read...
Forum: Ion Torrent 12-05-2017, 09:39 AM
Replies: 8
Views: 2,084
Posted By bvk
Thank you !! Our data is generated from Ion...

Thank you !! Our data is generated from Ion Torrent Amplicon based platform. Do you think Hisat can be used for that? And could you please tell what is the main difference between Ion torrent...
Forum: Ion Torrent 12-04-2017, 08:25 AM
Replies: 8
Views: 2,084
Posted By bvk
Thanks for the reply. But I see that Tophat and...

Thanks for the reply. But I see that Tophat and cufflinks pipeline cant be used for Ion torrent data right. Are you sure that I can use these tools?

Can I also use Hisat2, Stringtie and Ballgown? ...
Forum: Ion Torrent 12-04-2017, 07:48 AM
Replies: 8
Views: 2,084
Posted By bvk
Tools for Ion Torrent RNA-Seq data analysis

Hello Everyone,

I'm aware about the tools that need to be used for RNA-Seq data analysis of illumina platform.

But I would like to know what tools need to be used for RNA-Seq analysis of Ion...
Forum: Bioinformatics 07-20-2017, 03:42 AM
Replies: 1
Views: 611
Posted By bvk
Question about using limma for differential analysis

For the Differential analysis I'm using "limma" R package. I'm using RSEM log2 transformed counts data from XENA browser. A matrix "U" with 20,000 genes as rows and more than 300 samples as columns....
Forum: Bioinformatics 06-07-2016, 02:58 AM
Replies: 2
Views: 979
Posted By bvk
Thank you. So the GTF file has "LSU-rRNA_Hsa" and...

Thank you. So the GTF file has "LSU-rRNA_Hsa" and also "SSU-rRNA_Hsa". It means LSU rRNA: 5S, 5.8S, and 28S
SSU rRNA: 18 S

But the GTF file hg19 I'm using have 5S, LSU-rRNA_Hsa, SSU-rRNA_Hsa.
...
Forum: Bioinformatics 06-07-2016, 01:44 AM
Replies: 2
Views: 979
Posted By bvk
Cannot find 18s and 28s ribosomal RNAs in the GTF file from UCSC

Hello everyone,

I couldn't find 18s and 28s rRNA's in the GTF file from UCSC genome browser. I want to map against hg19/GRCh37 genome. Can anyone please tell me from where I can look up for 18s...
Forum: Bioinformatics 04-23-2016, 08:32 AM
Replies: 3
Views: 1,074
Posted By bvk
FoldChange calculation for two samples

Hi all,

I have two RNA-Seq samples. Detecting differential expressed genes for two samples is not possible. So, I want to calculate fold change for Sample1 vs Sample2.

Based on that I want to...
Forum: RNA Sequencing 04-20-2016, 07:15 AM
Replies: 22
Views: 3,034
Posted By bvk
Thanks a lot. Actually it is only to check...

Thanks a lot. Actually it is only to check whether rRNA depletion is done well or not.
Forum: RNA Sequencing 04-20-2016, 06:34 AM
Replies: 22
Views: 3,034
Posted By bvk
Differential expression is already done. But the...

Differential expression is already done. But the clients need the total information in a report. In that they also need the read counts aligned to different regions. I will ask the person again...
Forum: RNA Sequencing 04-20-2016, 06:04 AM
Replies: 22
Views: 3,034
Posted By bvk
what do you mean here (Does not help you if you...

what do you mean here (Does not help you if you actually were interested in rRNA.) I didn't get this. There are 246578 read pairs aligned to rRNA regions. Could you please tell clearly about the...
Forum: RNA Sequencing 04-20-2016, 05:52 AM
Replies: 22
Views: 3,034
Posted By bvk
OK. I used the same command. please have a look...

OK. I used the same command. please have a look and tell me.

featureCounts -p -t exon -g gene_id -a hg19_rRNA -o MCF10A_BaP_pool1_counts.txt MCF10A_BaP_pool1_R1_postTrimming/accepted_hits.bam
...
Forum: RNA Sequencing 04-20-2016, 05:29 AM
Replies: 22
Views: 3,034
Posted By bvk
Ok. But the featureCounts command is the same as...

Ok. But the featureCounts command is the same as given before? or it should be changed?
Forum: RNA Sequencing 04-20-2016, 05:23 AM
Replies: 22
Views: 3,034
Posted By bvk
When I gave that command it didn't give anything....

When I gave that command it didn't give anything. May be that gtf doesn't have any info regarding rRNA?
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