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Forum: RNA Sequencing 08-10-2017, 08:25 AM
Replies: 1
Views: 2,419
Posted By ronaldrcutler
Bump. I am also curious about this too. It...

Bump.

I am also curious about this too. It has been observed that the mean-varience relationship is approximately quadratic, while I also observe the dispersion parameter increase in genes with...
Forum: Bioinformatics 06-02-2017, 07:49 AM
Replies: 0
Views: 603
Posted By ronaldrcutler
Salmon: library type disagreement

Hi all,

I have been testing out salmon on RNA-seq data and am wondering what I should do about this output regarding library type. Basically, I set the expected library type to expect 'inward...
Forum: Bioinformatics 05-29-2017, 10:51 AM
Replies: 3
Views: 1,110
Posted By ronaldrcutler
Hi Gringer, The ID18_x were biological...

Hi Gringer,

The ID18_x were biological replicates from the same batch and GP18_x were biological replicates from the same batch. They did not come from the same samples or the same batch.

I...
Forum: Bioinformatics 05-24-2017, 11:21 AM
Replies: 3
Views: 1,110
Posted By ronaldrcutler
DESeq2 PCA Plots

Hello all,

I am running DESeq2 like so in R:

library(DESeq2)
sTable = data.frame(sampleName = files, fileName = files, condition = cond)
dds <- DESeqDataSetFromHTSeqCount(sampleTable =...
Forum: Bioinformatics 03-29-2017, 10:23 AM
Replies: 0
Views: 873
Posted By ronaldrcutler
Averaging TPM counts among replicates

Hello all,

I calculated TPM counts from an un-normalized HTSeq-count output file for a number of replicates. I am wondering how should I go about averaging these counts among replicates?
...
Forum: Bioinformatics 01-04-2017, 05:31 AM
Replies: 2
Views: 1,177
Posted By ronaldrcutler
Thanks Devon, helps a lot. I'll make sure to give...

Thanks Devon, helps a lot. I'll make sure to give featureCounts a go.
Forum: Bioinformatics 01-03-2017, 08:14 PM
Replies: 2
Views: 1,177
Posted By ronaldrcutler
Not 100% mapping in output bam?

Running samtools flagstat on a bam file resulting from alignment with Hisat2 gives:
76075665 + 0 in total (QC-passed reads + QC-failed reads)
1565341 + 0 secondary
0 + 0 supplementary
0 + 0...
Forum: Bioinformatics 12-24-2016, 08:00 AM
Replies: 0
Views: 2,327
Posted By ronaldrcutler
HTSeq-count: Warning: x reads with missing mate encountered.

As I am running through an RNA-Seq pipeline using Hisat2 for alignment and HTSeq-count for counting reads in features I notice this warning at the bottom of the log file
Warning: 284233 reads with...
Forum: Bioinformatics 12-21-2016, 01:45 PM
Replies: 3
Views: 1,796
Posted By ronaldrcutler
Thanks Genomax. I would assume in the Tophat2 run...

Thanks Genomax. I would assume in the Tophat2 run with these "recovered" files there were erroneous discordant alignments that would be discarded and not affect overall alignment.

I was...
Forum: Bioinformatics 12-21-2016, 10:50 AM
Replies: 3
Views: 1,796
Posted By ronaldrcutler
Hisat2: Differing amount of reads in mates

Hello all,

I am aligning paired-end reads using Hisat2. Unfortunately, some of the fastq files were corrupted in transfer. I was able to recover them using a gzip recovery protocol, but was left...
Forum: Introductions 12-21-2016, 09:48 AM
Replies: 5
Views: 1,327
Posted By ronaldrcutler
Figures 6B and 6C should answer the mate pair...

Figures 6B and 6C should answer the mate pair question: http://www.illumina.com/documents/products/datasheets/datasheet_genomic_sequence.pdf
Forum: Bioinformatics 10-31-2016, 07:48 AM
Replies: 16
Views: 5,809
Posted By ronaldrcutler
Thanks for the advice, using your edited command...

Thanks for the advice, using your edited command I get this error:Mismatch between length of bases and qualities for read 33584341 (id=J00138:68:HCWKCBBXX:3:2218:11728:42565 1:N:0:GAATTCGT+ACGTCCTG)....
Forum: Bioinformatics 10-28-2016, 10:29 AM
Replies: 16
Views: 5,809
Posted By ronaldrcutler
Full repair.sh command repair.sh...

Full repair.sh command
repair.sh in1=47_R1_001.fastq.gz_recovered in2=47_R2_001.fastq.gz_recovered out1=47_R1_001.fastq.gz_recovered_repaired out2=47_R2_001.fastq.gz_recovered_repaired...
Forum: Bioinformatics 10-28-2016, 10:19 AM
Replies: 16
Views: 5,809
Posted By ronaldrcutler
repair.sh

So I have run repair.sh with the default parameters on a pair of read files with this resulting error. I thought if repair.sh saw this, then it would just remove it?

Mismatch between length of...
Forum: Bioinformatics 10-28-2016, 10:00 AM
Replies: 16
Views: 5,809
Posted By ronaldrcutler
Thanks, worked well.

Thanks, worked well.
Forum: Bioinformatics 10-20-2016, 10:37 AM
Replies: 16
Views: 5,809
Posted By ronaldrcutler
Same Problem, different situation.

Hi Genomax,

I have the same error in a file of mine:
Error: qual length (214) differs from seq length (140) for fastq record !

When I try your suggested command on a file that has been having...
Forum: RNA Sequencing 10-20-2016, 10:07 AM
Replies: 1
Views: 2,572
Posted By ronaldrcutler
As suggested by GenoMax, try this command to...

As suggested by GenoMax, try this command to examine the offending record by pulling it out of the file
$ cat (or zcat) <fastq_file_name> | grep <sequence_identifier> -A 3
Forum: Bioinformatics 08-18-2016, 08:35 PM
Replies: 1
Views: 977
Posted By ronaldrcutler
De novo Assembly k-mer question

Hello all, I have a general discussion question:

If small kmers are used in an assembly that utilizes a de bruijn graph, we can expect to get many more contigs than we would if we used larger...
Forum: Bioinformatics 08-15-2016, 01:14 PM
Replies: 0
Views: 835
Posted By ronaldrcutler
GapCloser Output

Hello all,

Was wondering what was the meaning of this stdout from running GapCloser from SOAPdenovo

actual gap sum: 1965331
extend gap sum: 18802
actual gap count: 48
finish gap count: 5...
Forum: Bioinformatics 08-10-2016, 05:57 PM
Replies: 0
Views: 876
Posted By ronaldrcutler
GapCloser max read len?

Hello all,

Seeking to get clarification on the max read len parameter in GapCloser and why the limit is 155. For example, I am using reads sequenced on a miseq which are ~250 bp long.

Thanks
Forum: Bioinformatics 08-10-2016, 02:46 PM
Replies: 1
Views: 1,970
Posted By ronaldrcutler
Bump I would also appreciate this. Can't...

Bump

I would also appreciate this. Can't find it anywhere!
Forum: Bioinformatics 08-09-2016, 11:47 AM
Replies: 2
Views: 1,672
Posted By ronaldrcutler
Steps to install blat v34 on Mac OSX (10.10.5)

This is for Mac users who are using AlignGraph (https://github.com/baoe/AlignGraph) and want to use blat alignment which requires blat v34 (latest at the time of writing is blat v36)

Credit goes...
Forum: Bioinformatics 08-07-2016, 08:51 PM
Replies: 2
Views: 1,672
Posted By ronaldrcutler
Blat installation

Hello all,

I have been using AlingGraph to aling contigs I have to a reference genome. This program uses blat, however only supports up to version 34. I downloaded the blatSrc34.zip source code...
Forum: Bioinformatics 08-03-2016, 12:30 PM
Replies: 0
Views: 1,197
Posted By ronaldrcutler
SSPACE library file

Hello all,

I have been trying to use SSPACE for scaffolding contigs in a de novo assembly, but can't seem to get the library file right. Here is the terminal command and Error:
perl...
Forum: RNA Sequencing 08-03-2016, 12:22 PM
Replies: 3
Views: 1,661
Posted By ronaldrcutler
Also consider doing a quality analysis of your...

Also consider doing a quality analysis of your fastq files before doing any trimming or proceeding in the pipeline. Use FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) for the...
Showing results 1 to 25 of 80

 


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