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Forum: Bioinformatics 03-22-2017, 07:41 PM
Replies: 1
Views: 1,537
Posted By adrian
Tumor only BAM files for mpileup or varscan

Hi group,
I have ~100 tumor only BAM files from miSeq using panel of 20 genes amplicons. I used a GATK pipeline with mutect2 with tumor only option.

I want to run mpileup too and verify the...
Forum: Bioinformatics 01-26-2017, 11:57 AM
Replies: 0
Views: 1,186
Posted By adrian
How long miso --run would take for a single BAM file

Hi:
I am trying to estimate how much time MISO --run would take for a given bam file (5Gb) and on high performance cluster with over 60Gb ram.
I know there could be many parameters that would...
Forum: Bioinformatics 12-29-2016, 01:23 PM
Replies: 0
Views: 1,761
Posted By adrian
Cuffdiff error [bam_header_read] invalid BAM binary header (this is not a BAM file).

Dear Group,

I never came across errors in Tophat2/Cufflinks analysis and this error is troubling me and I cannot find a proper solution. I am posting in anticipation that I could get some help. ...
Forum: Bioinformatics 03-03-2016, 08:38 PM
Replies: 1
Views: 876
Posted By adrian
strand specific mayhem for Tophat and Cufflinks

Hi I have a strand specific RNA-Seq experiment. The libraries were prepared based on dUTP and I was told to use forward strand.

I used Tophat to align the fastq files and merged replicates. I get...
Forum: Bioinformatics 01-27-2016, 09:29 AM
Replies: 1
Views: 1,040
Posted By adrian
DESEQ2 design matrix help

Hello:

I have a complicated RNASeq experimental design and I need some help from experts.

my aim is to compare normal vs. tumor rna-seq data.

I have 4 different normal samples obtained...
Forum: Bioinformatics 09-10-2015, 12:56 PM
Replies: 2
Views: 928
Posted By adrian
get genes located in a genomic region

Hello:

I have a bed file of genomic coordinates in a file (# of rows in this file are 800).

chr5 87956489 87957187
chr16 89626644 89627869
chr17 72270301 72270512...
Forum: Bioinformatics 07-23-2015, 05:33 AM
Replies: 2
Views: 883
Posted By adrian
Any suggestions I appreciate.. thanks

Any suggestions I appreciate..
thanks
Forum: Bioinformatics 07-22-2015, 01:00 PM
Replies: 2
Views: 883
Posted By adrian
Merging RNA-Seq files run at two different times with identical setup

Hi group:
I am sure this question has been asked in many flavors but after pouring over those, I still could not get what exactly I am asking for. I thought members could provide an answer.

My...
Forum: Bioinformatics 05-28-2015, 07:28 AM
Replies: 0
Views: 844
Posted By adrian
Identifying substitutions in a region of BAM file

Hi group:

I am interested in finding substitutions in a read downstream of a particular site.

In detail:

My target region - chr2: 1200-2000.
CRISPR site: chr2:1220-1240

First, find the...
Forum: Bioinformatics 05-05-2015, 03:37 AM
Replies: 3
Views: 2,858
Posted By adrian
Yes thats a disadvantage I agree. ...

Yes thats a disadvantage I agree.

Unfortunately, the bam file does not have enough PE reads.

When I used bamtofastq for PE fastq files, interestingly I obtained 0 fastq reads.
Forum: Bioinformatics 05-05-2015, 02:38 AM
Replies: 3
Views: 2,858
Posted By adrian
converting paired-end (PE) bam file to single-end (SE) fastq

Hi:
while working with COAD TCGA BAM files, I find the very annoying to find PE reads. These files are mashed up and not consistent.
for example:
1. read lengths are not consistent. Some are 34...
Forum: Bioinformatics 04-25-2015, 02:27 PM
Replies: 0
Views: 2,129
Posted By adrian
calculating mutation burden per TCGA sample

Hi:

in TCGA breast data, I found using expression of genes of interest in the lab, ~120 samples segregate into two groups that have high and low expression of my gene.

I want to summarize...
Forum: Bioinformatics 03-18-2015, 03:29 PM
Replies: 1
Views: 724
Posted By adrian
integrated pathway identification

hello group,

What are the pathway analyses tools that can identify pathways affected given mutation, expression, methylation and copy number data, for example TCGA type data. I came across...
Forum: Bioinformatics 08-07-2014, 04:42 AM
Replies: 3
Views: 1,481
Posted By adrian
thank you. it was helpful

thank you. it was helpful
Forum: Bioinformatics 08-06-2014, 03:37 PM
Replies: 3
Views: 1,481
Posted By adrian
Getting gene coordinate not exons

Hi:
Is there a way to get gene coordinates rather exon coordinates for Hg19 as a bed file.

I do not want exon coordinates since it is repeating my values from a different file.

I want to...
Forum: Bioinformatics 07-02-2014, 12:19 PM
Replies: 0
Views: 642
Posted By adrian
Exon skips events in refseq

Hi:

Is it possible to get gene names and exon coordinates of all exon-skip events in RefSeq.

I am interested in getting a bed file:

Gene skip-exon-start skip-exon-end ...
Forum: Bioinformatics 06-30-2014, 09:12 AM
Replies: 5
Views: 2,035
Posted By adrian
Thank you so much! that is helpful. However...

Thank you so much! that is helpful.

However when I use the following I don't see files - known.gff, known.fa, known.fa.tlst, known.fa.ver and the known.* Bowtie index files in the directory.
...
Forum: Bioinformatics 06-27-2014, 07:11 PM
Replies: 5
Views: 2,035
Posted By adrian
shorter time for building bowtie index

Hi:
I am not sure if this question has been asked before.

I have 120 RNA-Seq fasta files. I am using tophat2 for aligning to human genome.

I am queing this job on a 70 node cluster. I am...
Forum: Bioinformatics 06-25-2014, 04:47 PM
Replies: 3
Views: 3,460
Posted By adrian
Thank you!

Thank you!
Forum: Bioinformatics 06-18-2014, 03:51 PM
Replies: 3
Views: 3,460
Posted By adrian
How can I add NH:i:1 tag for every uniquely mapped read from BWA

Hi:

I have a BWA aligned BAM file. This BWA generated BAM file does not have NH:i:1 tag.

My aim is to create a BAM file where read is mapped uniquely and add NH:i:1 tag at the end of read.
...
Forum: Bioinformatics 06-07-2014, 08:22 AM
Replies: 4
Views: 2,580
Posted By adrian
Thank you. Is there a particular function that...

Thank you.
Is there a particular function that I could use? If not what would be the logic to get those read stats.

thanks
Adrian
Forum: Bioinformatics 06-06-2014, 12:43 PM
Replies: 4
Views: 2,580
Posted By adrian
Bam file to junctions.bed

Hi:

I received aligned BAM file and do not have a raw sequence file.

My aim is to count how many reads skip exon 7 of a gene and how many reads do not skip, in addition to reads that span exons...
Forum: Bioinformatics 04-17-2014, 05:44 AM
Replies: 4
Views: 1,691
Posted By adrian
Thanks for replies. I got it.

Thanks for replies. I got it.
Forum: Bioinformatics 04-16-2014, 03:06 PM
Replies: 4
Views: 1,691
Posted By adrian
RNA-Seq sequence counts fastq and BAM files

Hi:
I am a bit confused about total number of reads obtained from RNA-Seq run.

In the case of a paired end run fastq should both R1 and R2 reads be counted to get total number of reads.
...
Forum: Bioinformatics 01-30-2014, 03:13 PM
Replies: 0
Views: 897
Posted By adrian
junction reads

Is there a tool to process tcga splice junction reads from rna-seq either to visualize in the context of splicing or find differential expression between exons.
thanks
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