SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 22 of 22
Search took 0.00 seconds.
Search: Posts Made By: RemitoAmigo
Forum: De novo discovery 12-20-2016, 05:20 PM
Replies: 2
Views: 6,963
Posted By RemitoAmigo
possible solution

it was an encoding issue for me with the in_groups.csv and in_libs.csv file. If you test with this, ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/
(see test.genome.tar.gz) and it...
Forum: Sample Prep / Library Generation 06-14-2016, 08:36 AM
Replies: 1
Views: 1,526
Posted By RemitoAmigo
Hi Reza, Interesting...I was about to try...

Hi Reza,

Interesting...I was about to try something as well with the i7s of the Truseq HT kit....I didn't know about the Bioo kits.

Yes, they are 6bp in length.

Were you able to sequence...
Forum: Illumina/Solexa 06-04-2015, 10:28 AM
Replies: 1
Views: 1,445
Posted By RemitoAmigo
nextSeq500 heat output

Hi guys,

I'm trying to prep the site for a Nextseq 500, the room is quite small. In the prep guide, they say that the instrument generates 600W of heat.

My question: Is there a fan vent at the...
Forum: RNA Sequencing 03-26-2015, 12:31 PM
Replies: 0
Views: 1,120
Posted By RemitoAmigo
mRNA rat liver Torrent library on tapeStation

Hey Guys,

Any one of you has seen a shoulder(left side of library) like this for mRNA on the tapeStation?

It is not adapter dimers as sometime I get them and they are much smaller in size....
...
Forum: Ion Torrent 03-09-2015, 04:57 AM
Replies: 2
Views: 2,859
Posted By RemitoAmigo
Hi, adapters, key sequences, barcodes?

Hi,

adapters, key sequences, barcodes?
Forum: Ion Torrent 10-24-2014, 09:37 AM
Replies: 2
Views: 5,619
Posted By RemitoAmigo
Hi-q

Hi guys,

I know that the HI-Q seq enzyme is available for the PGM...any impressions?

Remito
Forum: Sample Prep / Library Generation 09-09-2014, 08:32 AM
Replies: 7
Views: 3,671
Posted By RemitoAmigo
Good question, if the poly A failed...I think you...

Good question, if the poly A failed...I think you would see anything...because you would of most likely thrown everything out. A bit of adapters maybe!?
Forum: Sample Prep / Library Generation 09-08-2014, 08:18 AM
Replies: 7
Views: 3,671
Posted By RemitoAmigo
Have you done a Pico on the bionanalyser after...

Have you done a Pico on the bionanalyser after your polyA selection and fragmentation?

Remito
Forum: Sample Prep / Library Generation 09-04-2014, 11:27 AM
Replies: 7
Views: 3,671
Posted By RemitoAmigo
NEBNext poly(A) mRNA magnetic isolation module

Hi guys,

NEBNext poly(A) mRNA magnetic isolation module

Did anyone tried this? impressions? results?

Tx.

Remito
Forum: Ion Torrent 09-01-2014, 02:32 PM
Replies: 2
Views: 1,939
Posted By RemitoAmigo
reply

Hi super,

What seems normal for RNA is your figure2..where the IonXpress barcodes are listed.

You should have links at the bottom of the report for .bam files for each barcodes which you can...
Forum: Ion Torrent 08-15-2014, 12:10 PM
Replies: 4
Views: 2,569
Posted By RemitoAmigo
Have you done by any chance a Qbit on your...

Have you done by any chance a Qbit on your unenriched template?
Low number for both dyes, could mean that you have lost some beads in the process prior to running the ES.

Remito
Forum: Bioinformatics 05-26-2014, 08:28 AM
Replies: 4
Views: 9,692
Posted By RemitoAmigo
Keep also in mind...this was Ribo Zero...All...

Keep also in mind...this was Ribo Zero...All sorts of RNAs are in there...
I would expect PolyA selection to be higher (mapping to exons)...but that's just me thinking...

Remi
Forum: Ion Torrent 04-30-2014, 11:10 AM
Replies: 14
Views: 7,432
Posted By RemitoAmigo
I'm using STAR + bowtie right now and getting 75%...

I'm using STAR + bowtie right now and getting 75% alignment on mouse ref. But I'll definitively give a try to GSNAP.

Tx.

RemitoAmigo
Forum: Ion Torrent 04-30-2014, 05:57 AM
Replies: 14
Views: 7,432
Posted By RemitoAmigo
Hi guys, We have about 10 successful run for...

Hi guys,

We have about 10 successful run for RNA seq on the proton. We use the RNA-seq v2 kit from Life tech. Both Ribo- and Ribo gold and RNaseIII fragmentation and (chemical from NEB). We also...
Forum: Ion Torrent 03-06-2014, 04:02 PM
Replies: 0
Views: 2,153
Posted By RemitoAmigo
RNA-Seq barcodes on Ion Torrent

Hi Guys,

We're experiencing difficulties....with RNA seq

We start with the fragmented RNA ~30ng(according to the Pico Bioanalyzer chip), build the library with the AB lib builder then amplify...
Forum: Sample Prep / Library Generation 01-27-2014, 10:35 AM
Replies: 0
Views: 1,268
Posted By RemitoAmigo
Pipetter Robot for sample prep, library, etc.

Hi guys,

I'm considering the Pipetmax for our lab...Anyone here has one? Strong points, weak points? Comments?

Here we focus a lot on RNA seq...

RemitoAmigo
Forum: Ion Torrent 01-27-2014, 10:17 AM
Replies: 19
Views: 7,048
Posted By RemitoAmigo
Far from being a master in the field...Have you...

Far from being a master in the field...Have you had a look at Ion Reporter?
Forum: RNA Sequencing 10-23-2012, 01:15 PM
Replies: 8
Views: 2,216
Posted By RemitoAmigo
Hi Ramma, Here's the inversion... 1st...

Hi Ramma,

Here's the inversion...
1st read: chr1 3127915 0 100M = 3127918
2nd read: chr1 3127918 0 100M = 3127915

From the SAM Format Specification document: "Reads/segments having identical...
Forum: RNA Sequencing 10-23-2012, 12:12 PM
Replies: 8
Views: 2,216
Posted By RemitoAmigo
Hi Ramma, The SAM file is generated with...

Hi Ramma,

The SAM file is generated with Samtools view...from the BAM that was generated by tophat..

You're looking at a sample of my SAM file where 2 entries have the same Qname but positions...
Forum: RNA Sequencing 10-23-2012, 11:54 AM
Replies: 8
Views: 2,216
Posted By RemitoAmigo
Hi Ramma, So seeing these kinds of things in...

Hi Ramma,

So seeing these kinds of things in the SAM file is normal? i.e. having the same Qname X2 and positions inverted? I have this for so many reads....
...
Forum: RNA Sequencing 10-22-2012, 08:22 PM
Replies: 8
Views: 2,216
Posted By RemitoAmigo
-Update There is a lot of QName duplicates...

-Update

There is a lot of QName duplicates with the only difference being the TLEN (one positive and one negative)

Any reasons why would I have so many duplicates?
Forum: RNA Sequencing 10-22-2012, 07:34 PM
Replies: 8
Views: 2,216
Posted By RemitoAmigo
Output Alignment of TopHat 2X the number of left and right reads

Hi Guys,

I don't get it..here's the prep read info from tophat 2.04

left_min_read_len=100
left_max_read_len=100
left_reads_in =15696378
left_reads_out=15695101
right_min_read_len=100...
Showing results 1 to 22 of 22

 


All times are GMT -8. The time now is 03:49 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO