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Search: Posts Made By: imsharmanitin
Forum: Bioinformatics 07-09-2018, 08:53 AM
Replies: 1
Views: 1,297
Posted By imsharmanitin
Understanding Read Groups for single end and paired end data

Dear All,

I am new to GATK and very confused regarding "Read Groups". I have fastq files and I will like to add read groups to the files. This is what I have understood and please do let me know...
Forum: RNA Sequencing 06-15-2017, 01:59 PM
Replies: 2
Views: 2,358
Posted By imsharmanitin
is this a technical replicate or biological replicate

i know that biological replicate is one taken from different organism/sample while technical replicate is one from same organism/sample.

However, I am not able to understand that a cell line...
Forum: Bioinformatics 05-23-2017, 03:51 PM
Replies: 0
Views: 1,739
Posted By imsharmanitin
Aggregated transcripts by Salmon and simplesum_avetxl used in TXIMPORT

I am new in the field on RNA-Seq analysis and trying to understand the methodology behind Salmon's aggregation of transcripts into gene level.

From the forum...
Forum: RNA Sequencing 03-30-2016, 02:39 AM
Replies: 5
Views: 3,134
Posted By imsharmanitin
Michael, thanks for the clarification. ...

Michael, thanks for the clarification.

Cheers,
Nitin
Forum: RNA Sequencing 03-30-2016, 02:25 AM
Replies: 5
Views: 3,134
Posted By imsharmanitin
One more query will the chromosome sizes,...

One more query will the chromosome sizes, mentioned in links present in the quoted text, will be same for all the releases of GRCh38 i.e. GRCh38.76 which was first one to GRCh38.84 the latest one?
...
Forum: RNA Sequencing 03-29-2016, 05:35 PM
Replies: 5
Views: 3,134
Posted By imsharmanitin
Richard thanks a ton Nitin

Richard thanks a ton

Nitin
Forum: RNA Sequencing 03-29-2016, 05:14 PM
Replies: 5
Views: 3,134
Posted By imsharmanitin
Exclamation Chrom Sizes for Ensembl Reference

i want to convert BAM to BigWig for ensembl reference genome (Homo_sapiens.GRCh38.81.fa to be specific) using the following work flow.

Workflow:
# 1. Convert SAM to BAM
samtools view -S -b -o...
Forum: Site Feedback/Suggestions 08-12-2015, 03:11 AM
Replies: 11
Views: 9,052
Posted By imsharmanitin
i posted same post both on biostars and...

i posted same post both on biostars and seqanswers without knowing the fact that posts can't be deleted on seqanswers.

i think post deletion should be allowed in certain cases. a person can send...
Forum: Bioinformatics 08-11-2015, 08:03 AM
Replies: 1
Views: 840
Posted By imsharmanitin
Arrow DESeq2 model design: dose and time effect

i have three samples each with 3 biological replicates i.e. one control and other at dose 12ug/ml and 25ug/ml at 24hr

> library('DESeq2')

> directory<-"./data"

> sampleFiles <-...
Forum: RNA Sequencing 07-28-2015, 08:08 AM
Replies: 1
Views: 2,205
Posted By imsharmanitin
Cool Differential expression using TopHat/Cufflinks, analysis by CumeRbund

I am trying to do differential expression analysis for 6 samples with no replicates

The protocol used by me after following several threads and...
Forum: RNA Sequencing 07-01-2015, 09:29 AM
Replies: 1
Views: 1,036
Posted By imsharmanitin
Cool TopHat -M/--prefilter-multihits; unmapped reads

hi!

i am confused when to use TopHat "-M/--prefilter-multihits and when not

"When mapping reads on the transcriptome, some repetitive or low complexity reads that would be discarded in the...
Forum: Bioinformatics 06-30-2015, 04:43 PM
Replies: 4
Views: 2,735
Posted By imsharmanitin
If i understood correctly, when we use the...

If i understood correctly, when we use the --transcriptome-index without -T then the reads will be first mapped to the transcriptome-index and the reads which fail to match will be mapped to genome...
Forum: Bioinformatics 06-30-2015, 03:18 PM
Replies: 3
Views: 2,101
Posted By imsharmanitin
i was asking about the data that came from a...

i was asking about the data that came from a standard library protocol.

i asked the service provider about the protocol used to generate the reads. this is the response from them

"samples have...
Forum: Bioinformatics 06-30-2015, 10:08 AM
Replies: 3
Views: 2,101
Posted By imsharmanitin
library type for single end RNA-seq data

I searched lot of threads but didn't find any concrete answer.

I have single end RNA-seq data generated by on a Hi-Seq 2000 and I am not sure if there is some strand information associated with...
Forum: Bioinformatics 06-30-2015, 05:07 AM
Replies: 4
Views: 2,735
Posted By imsharmanitin
so this will be the workflow: 1) generate...

so this will be the workflow:

1) generate whole genome index using bowtie2
Homo_sapiens.GRCh37.75.dna.primary_assembly.fa
Homo_sapiens.GRCh37.75.gtf


2) the using tophat 2 to create a...
Forum: Bioinformatics 06-30-2015, 03:38 AM
Replies: 4
Views: 2,735
Posted By imsharmanitin
transcriptome_index Bowtie2 Index

Dear all,

As far as understand Tophat2 creates an transcriptome_index which also includes Bowtie2 Index files using GTF and the genome file. Then why do we need to supply Bowtie2 Index to create...
Forum: RNA Sequencing 06-24-2015, 09:01 AM
Replies: 1
Views: 2,234
Posted By imsharmanitin
Cool processing Fastq files from HiSeq2000 single end and RNAseq analysis

Hello all,

i apologise in advance for asking some basic questions

i have recently started working on RNA-Seq. i have fastq files in zipped format.

I read lot of threads and the one that...
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