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Forum: Bioinformatics 01-30-2017, 10:54 AM
Replies: 3
Views: 2,213
Posted By liguow
It further confirms my hypothesis. Pysam tried to...

It further confirms my hypothesis. Pysam tried to retrieve the reference allele from FASTA file, it reported this error message when it failed to find
'chr10_NT_461738v1_random'.
Forum: Bioinformatics 01-30-2017, 06:16 AM
Replies: 3
Views: 2,213
Posted By liguow
The error message "sequence...

The error message "sequence 'chr10_NT_461738v1_random' not present" was not issued by CrossMap itself, it could be issued by its dependent package like pysam.

My guess is...
Forum: Bioinformatics 05-24-2016, 06:58 AM
Replies: 1
Views: 1,408
Posted By liguow
There must be very big number(s) in your BED...

There must be very big number(s) in your BED file. If you are working on human/mouse genome, you must have made some mistakes during the preparation of this BED file. However, if you are working on...
Forum: RNA Sequencing 11-10-2014, 09:57 AM
Replies: 1
Views: 1,964
Posted By liguow
The "first strand" or "second strand" you...

The "first strand" or "second strand" you mentioned also confused me, the two ends (i.e. read1 and read2) were generated from the same RNA fragment, if one read was stranded, the other read was also...
Forum: Bioinformatics 11-20-2013, 07:43 PM
Replies: 5
Views: 4,313
Posted By liguow
CrossMap

CrossMap is a program for convenient conversion of genome coordinates between assemblies. It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.
...
Forum: Bioinformatics 02-04-2013, 11:24 AM
Replies: 19
Views: 15,712
Posted By liguow
Interesting. I used it without any problem (I am...

Interesting. I used it without any problem (I am using python2.7). And, if you can download it, you can do whatever you want.
Forum: Bioinformatics 10-23-2012, 06:06 AM
Replies: 6
Views: 2,549
Posted By liguow
Not yet. The manuscript is under review now.

Not yet. The manuscript is under review now.
Forum: Bioinformatics 07-11-2012, 12:59 PM
Replies: 6
Views: 2,549
Posted By liguow
Most straightforward way is not to use phyloCSF....

Most straightforward way is not to use phyloCSF. Instead, using PCAT, you only need the mRNA sequence or genome coordinates (which you already have if you already rebuild the transcriptome)...
Forum: Bioinformatics 04-20-2012, 09:12 AM
Replies: 9
Views: 4,253
Posted By liguow
Maybe you can try "read_distribution.py" in RSeQC...

Maybe you can try "read_distribution.py" in RSeQC package to reaffirm this observation. You are expecting to see higher coverage in both 3'UTR and 5'UTR than the internal CDS exons.
Forum: Bioinformatics 03-29-2012, 12:45 PM
Replies: 19
Views: 15,712
Posted By liguow
Surprisingly to find that this problem is still...

Surprisingly to find that this problem is still not well resolved.

I write a python program "bam2wig.py" that is specially designed for RNA-seq, so it works fine for spliced read, for both...
Forum: RNA Sequencing 11-01-2011, 12:47 PM
Replies: 9
Views: 7,366
Posted By liguow
EVER-seq (Evaluate Experiment of RNA-seq)

fastqc only check the quality of sequence per se (such as GC content, base calling quality, over represented kmer, etc), that's fundamental and important. However, fastqc does not tell you if the...
Forum: Illumina/Solexa 12-31-2009, 08:29 AM
Replies: 15
Views: 6,711
Posted By liguow
exome sequencing

It might be this paper:
Title: Targeted capture and massively parallel sequencing of 12 human exomes

Nature 461, 272-276 (10 September 2009) | doi:10.1038/nature08250; Received 5 June 2009;...
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