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Search: Posts Made By: rnaeye
Forum: Bioinformatics 05-06-2017, 04:58 PM
Replies: 2
Views: 1,855
Posted By rnaeye
Hi GenoMax, Thank you for the answer at both...

Hi GenoMax,
Thank you for the answer at both sites. I checked the paper again, and finally found description of the reads. They did 150 bp paired end sequencing. They must have prepared the files...
Forum: Bioinformatics 05-06-2017, 08:01 AM
Replies: 2
Views: 1,855
Posted By rnaeye
Help needed with fastq-dump (SRA toolkit)

Hi
I am trying to split an .sra file into R1.fastq and R2.fastq However, I am getting single file, and I think forward and reverse reads are joined. Here is the accession number: SRR5439504.sra
...
Forum: RNA Sequencing 01-15-2016, 07:02 PM
Replies: 1
Views: 1,221
Posted By rnaeye
You can easily check directionality by the...

You can easily check directionality by the following tool
infer_experiment.py from http://rseqc.sourceforge.net/

bamtools stats command should tell you if you are paired o single end I believe....
Forum: Bioinformatics 12-03-2015, 08:46 AM
Replies: 2
Views: 2,022
Posted By rnaeye
Exactly what I was looking for, BBMap. Thanks...

Exactly what I was looking for, BBMap. Thanks GenoMax!
Forum: Bioinformatics 12-03-2015, 07:30 AM
Replies: 2
Views: 2,022
Posted By rnaeye
Coverage plots with inferred fragment sequence from PE reads

Hi!,
I need to make coverage plots/GC bias plots with inferred sequences from Illumina paired-end sequences. Someone here posted that he or she wrote a tool for this purpose. I am wondering if...
Forum: Illumina/Solexa 11-30-2015, 02:01 PM
Replies: 13
Views: 5,381
Posted By rnaeye
Thanks for correcting kmcarr. It was an...

Thanks for correcting kmcarr. It was an incomplete post by me.
Forum: Illumina/Solexa 11-30-2015, 09:20 AM
Replies: 13
Views: 5,381
Posted By rnaeye
I do not think dark cycles count against total...

I do not think dark cycles count against total number of reagents. I could do 72 cycle sequencing (2 x 33 cycles) + 6 cycle barcode = 72 cycles. This is with 50 cycle Illumina kit cartridge.
Forum: Bioinformatics 11-09-2015, 06:18 AM
Replies: 3
Views: 2,867
Posted By rnaeye
Thanks Philip. It's not too late. It's good to...

Thanks Philip. It's not too late. It's good to check the same thing with different approaches. I wil give a try. Best,
Forum: Bioinformatics 08-13-2015, 08:21 AM
Replies: 1
Views: 1,281
Posted By rnaeye
Of course it's possible. You can use...

Of course it's possible. You can use "bedtools."
Forum: Bioinformatics 08-13-2015, 08:15 AM
Replies: 7
Views: 3,213
Posted By rnaeye
bedtools coverage tool may help. ...

bedtools coverage tool may help.
http://bedtools.readthedocs.org/en/latest/content/tools/coverage.html
Forum: Bioinformatics 04-18-2015, 06:15 AM
Replies: 2
Views: 1,970
Posted By rnaeye
How to filter paired reads that are not mapped?

Hi!,
This should be very easy but it's confusing to me. I would appreciate some help. I have paired end Illumina sequencing. I want to keep only *unmapped* reads. Additionally, if one of the mates...
Forum: Illumina/Solexa 02-05-2015, 09:42 AM
Replies: 1
Views: 898
Posted By rnaeye
Most likely, it does not matter what kit, as long...

Most likely, it does not matter what kit, as long as kit has an end repair step. I have been using NEB's kits for complex and PCR DNA without any problem.
Forum: Sample Prep / Library Generation 10-03-2014, 07:45 AM
Replies: 2
Views: 1,074
Posted By rnaeye
If you are using antibodies used before in other...

If you are using antibodies used before in other publications, I would recommend you to read these articles. The same applies to specific protein you are trying to pull down. Amount of DNA you will...
Forum: Sample Prep / Library Generation 09-18-2014, 02:10 PM
Replies: 7
Views: 1,386
Posted By rnaeye
What are trying to achieve exactly?

What are trying to achieve exactly?
Forum: Bioinformatics 09-01-2014, 08:29 AM
Replies: 8
Views: 4,886
Posted By rnaeye
You can call samtools command from a Perl script...

You can call samtools command from a Perl script that also counts the lines.
Forum: Sample Prep / Library Generation 08-12-2014, 05:51 PM
Replies: 5
Views: 4,316
Posted By rnaeye
Yes, it's compatible with Miseq. You do not need...

Yes, it's compatible with Miseq. You do not need separate primers. You can give them a call to double check if you like.
Forum: Bioinformatics 08-11-2014, 08:07 PM
Replies: 12
Views: 3,688
Posted By rnaeye
sed 's/>//' inputFile | awk '{print...

sed 's/>//' inputFile | awk '{print ">"NR"\n"$0}'
Forum: Sample Prep / Library Generation 07-25-2014, 07:47 AM
Replies: 11
Views: 5,960
Posted By rnaeye
Are you using the same PCR polymerase/buffer. I...

Are you using the same PCR polymerase/buffer. I know that having proteins like BSA in the sample causes haze during Ampure cleanup. I cannot explain why your problem disappears with MQ water though.
Forum: Sample Prep / Library Generation 06-27-2014, 08:43 AM
Replies: 2
Views: 2,563
Posted By rnaeye
Leave the DNA at 55C for several hours or longer....

Leave the DNA at 55C for several hours or longer. Or you can leave at 37C overnight. I would add some EDTA in it though (0.1-1mM final concentration) High molecular weight genomic DNA takes time to...
Forum: Illumina/Solexa 06-19-2014, 03:51 AM
Replies: 11
Views: 8,144
Posted By rnaeye
Hi! concitacantarella, I have tried NEB's...

Hi! concitacantarella,
I have tried NEB's NEBNext Microbiome DNA Enrichment Kit. It also enriches for mitochondrial DNA since methylation is very low or absent in mito genome.
Forum: Illumina/Solexa 06-09-2014, 08:45 AM
Replies: 3
Views: 3,631
Posted By rnaeye
hi nucacidhunter, Truseq DNA Adapter sequences...

hi nucacidhunter,
Truseq DNA Adapter sequences are not same as small RNA adapter sequences. It's a small RNA library, except that inserts are not ~22nt small RNA but 200 bp long RNA. I think I have...
Forum: Illumina/Solexa 06-09-2014, 06:27 AM
Replies: 3
Views: 3,631
Posted By rnaeye
Can small RNA library be sequenced paired end?

Hi all,
I made a library that is compatible with TruSeq Small RNA protocol. In other words, I can sequence it by Miseq using small RNA sequencing option. My libraries contain longer inserts about...
Forum: Bioinformatics 06-08-2014, 06:35 AM
Replies: 6
Views: 2,803
Posted By rnaeye
You can take your bam file convert it to...

You can take your bam file convert it to samformat using bamtools then sort it by position, then use Unix uniq command with -c option on position column.
Forum: Bioinformatics 05-29-2014, 11:28 AM
Replies: 5
Views: 3,808
Posted By rnaeye
I think they have Nature Methods paper published...

I think they have Nature Methods paper published on it. I believe they are mapping to unique regions of each species. It may not give very accurate information on absolute and relative levels. I am...
Forum: Illumina/Solexa 05-17-2014, 02:19 PM
Replies: 21
Views: 14,981
Posted By rnaeye
Hi! If you are fine getting index reads as a...

Hi!
If you are fine getting index reads as a separate fastq file, Miseq has an option to turn it on. If you turn on relevant flag, it will print fastq files for each indices as well as reads. It's...
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