Forum: Bioinformatics
07-19-2017, 12:13 PM
|
|
Replies: 0
Views: 769
RNAseq bam to variants calling (GATK, Mutect1/2
Has anyone prepped rnaseq bam files for mutect/gatk? i found some pdf with pipeline schematics, but could not understand step by step prep. what are tools/settings needed to preprocess bam for...
|
|
Forum: Bioinformatics
08-05-2014, 07:12 AM
|
|
Replies: 4
Views: 1,592
1) RNA was qced using Nanodrop + 2d gel
2)...
1) RNA was qced using Nanodrop + 2d gel
2) Whole reads are polyA (or T), both on 50bp SE (HiSeq) and 250bp(MiSeq, did it just out of curiosity as a part of other run). mRNA polyA is between...
|
|
Forum: Bioinformatics
08-04-2014, 09:32 AM
|
|
Replies: 4
Views: 1,592
A lot of Poly-A after RNAseq completed
Hi,
Is there any obvious explanation why there would be a lot (~50%) of poly-A (or Poly-T, since this was bidirectional lib prep) in the output ?
RNA was purified using Poly-A+ enrichment (purified...
|
|
Forum: Illumina/Solexa
03-06-2014, 10:46 AM
|
|
Replies: 0
Views: 1,246
ChIPseq - how to qc the results ?
Hi,
I just received our first chipseq sequencing results. I tried to use 2 packages to get the interesting peaks (MACS and Homer). Homer produces various qc graphs that seem to be fine,...
|
|
Forum: Sample Prep / Library Generation
02-23-2014, 07:42 AM
|
|
Replies: 0
Views: 1,169
|
|
Forum: Illumina/Solexa
02-12-2014, 08:18 PM
|
|
Replies: 37
Views: 42,907
I always use the following formula and it never...
I always use the following formula and it never let me down. It considers that the complete length of Your library (on average) is ~350bp (~250bp insert + 100bp adaptors). After pooling of samples...
|
|
Forum: Illumina/Solexa
10-31-2013, 09:05 AM
|
|
Replies: 1
Views: 1,536
lack of blocking primer in pre and post hyb...
Hi,
It looks like I made a mistake in the hybridization library prep. Following the Rohland2012 protocol I forgot to use truncaded primers for pre-hyb (6 cycles). I used the fully indexed and flow...
|
|
Forum: Illumina/Solexa
08-01-2013, 11:25 AM
|
|
Replies: 7
Views: 9,281
|
|
Forum: Illumina/Solexa
07-31-2013, 07:53 PM
|
|
Replies: 7
Views: 9,281
|
|
Forum: Illumina/Solexa
07-31-2013, 07:49 PM
|
|
Replies: 0
Views: 2,244
Best method/kit for rRNA depletion
I am looking for a lib prep for RNAseq. It seems that rRNA is a crucial step (plant/human). What would You recommend ? Is there any way to do inhouse rRNA depletion (no commercial kit) ? Can You do...
|
|
Forum: Illumina/Solexa
07-17-2013, 11:01 AM
|
|
Replies: 30
Views: 26,829
|
|
Forum: Illumina/Solexa
07-17-2013, 10:52 AM
|
|
Replies: 2
Views: 1,265
Based on TruSeq library, You absolutely have to...
Based on TruSeq library, You absolutely have to run it the same day after multiplexing is finished. This will ensure ~800k/mm2 clusters. We noticed that running the very same sample (stored on SGP,...
|
|
Forum: Illumina/Solexa
07-11-2013, 12:05 PM
|
|
Replies: 2
Views: 2,218
MiSeq vs RNAseq
I have a technical question - why longer PE reads are not considered better for RNAseq. Since MiSeq can produce ~7-8Gbp, 25million 250 PE reads should equal 125million 50 PE reads....whats the...
|
|
Forum: Illumina/Solexa
06-10-2013, 07:51 AM
|
|
Replies: 24
Views: 9,554
@ MLog
When this problem arises, usually the...
@ MLog
When this problem arises, usually the flow cell is not seated properly. You have to open the flow cell compartment and re-seat the flow cell. If there was a spill all over the flow cell, You...
|
|
Forum: Illumina/Solexa
03-07-2013, 12:18 PM
|
|
Replies: 24
Views: 9,554
what is more interesting. If I used i7 barcode...
what is more interesting. If I used i7 barcode (index1):
Reverse primer used to enrich:
caagcagaagacggcatacgagatCCTGCGAcggtctcggcattcctgctgaacc
Do I have to use custom index1 primer to read it...
|
|
Forum: Illumina/Solexa
03-07-2013, 10:35 AM
|
|
Replies: 24
Views: 9,554
|
|
Forum: Illumina/Solexa
03-07-2013, 10:24 AM
|
|
Replies: 24
Views: 9,554
|
|
Forum: Illumina/Solexa
03-07-2013, 10:02 AM
|
|
Replies: 24
Views: 9,554
|
|
Forum: Illumina/Solexa
03-06-2013, 07:17 PM
|
|
Replies: 24
Views: 9,554
|
|
Forum: Illumina/Solexa
03-06-2013, 01:50 PM
|
|
Replies: 24
Views: 9,554
|
|
Forum: Illumina/Solexa
03-06-2013, 01:29 PM
|
|
Replies: 24
Views: 9,554
Stopped MiSeq run
Hi,
I experienced first problems with our MiSeq. This morning with new run loaded there was a flow rate error - first thought, valve.....
Did re-test at 250ul (failed) and 500ul (machine freezed)...
|
|
Forum: Bioinformatics
02-11-2013, 12:36 PM
|
|
Replies: 2
Views: 1,737
|
|
Forum: Bioinformatics
02-08-2013, 08:49 AM
|
|
Replies: 2
Views: 1,176
|
|
Forum: Illumina/Solexa
02-06-2013, 01:03 PM
|
|
Replies: 5
Views: 3,863
|
|
Forum: Illumina/Solexa
02-06-2013, 12:38 PM
|
|
Replies: 5
Views: 3,863
Demultiplexing MiSeq run reads.
Hi,
I have added indexing sequence along the regular target (at both P5 and P7, but only P5 had unique index, low plexity 20 amplicons). How to demultiplex it outside of MiSeq control ? These are...
|
