User: david.4.ray

gravatar for david.4.ray
david.4.ray10
Reputation:
10
Status:
New User
Location:
United States
Last seen:
6 months, 3 weeks ago
Joined:
4 years, 2 months ago
Email:
d**********@gmail.com

Posts by david.4.ray

<prev • 8 results • page 1 of 1 • next >
0
votes
1
answer
2.0k
views
1
answers
Comment: C: How do I pass options to pybedtools getfasta
... Please ignore this question. I found my problem. The strand information (+ or -) was in the wrong column of my bed file. ...
written 7 months ago by david.4.ray10
0
votes
1
answer
2.0k
views
1
answers
Comment: C: How do I pass options to pybedtools getfasta
... I appreciate this question and answer. It's been helpful as I try to learn how to use pybedtools. However, I'm having the same problem. The extracted sequences are not being reverse complemented. How was this resolved? My code is as follows: SLOPBED = BedTool('tmpbedfiles/' + QUERY + '.slop') F ...
written 7 months ago by david.4.ray10
0
votes
1
answer
3.0k
views
1
answers
Comment: A: [bcf_sync] incorrect number of fields (0 != 5) at 0:0
... Update: I ran `head` and `tail` on my .vcf file and it doesn't look so good after all. head yields what you would expect. Standard headers and such. tail does something very strange. In fact, it appears to be trying to read a binary rather than a text file. No idea where this development is arisi ...
written 3.8 years ago by david.4.ray10 • updated 14 months ago by RamRS25k
1
vote
1
answer
3.0k
views
1
answer
[bcf_sync] incorrect number of fields (0 != 5) at 0:0
... I am attempting to call variants on some genomes and troubleshooting an error I'm getting from bcftools. My commands are as follows: $SAMTOOLS_HOME/samtools mpileup -Q30 -C50 \ -uf $REF_HOME/$REFGENOME$INPUT/$SPECIES"_R3_noDup.bam" \ >$SPECIES"_mPileUp.vcf" Followed by: ...
software error genome samtools snp bcftools written 3.8 years ago by david.4.ray10 • updated 9 months ago by zx87548.7k
0
votes
1
answer
3.5k
views
1
answers
Comment: C: BWA MEM indexing
... Yep.  That was it.  Working just fine now. ...
written 4.2 years ago by david.4.ray10
0
votes
1
answer
3.5k
views
1
answers
Comment: C: BWA MEM indexing
... No. I have actually performed a full reference-based assembly of the genome using these reads. I'll explain. We have a working pipeline that will index the reference genome, then process the raw reads from the genome we want to assemble using that reference. One of the processing steps is to use tr ...
written 4.2 years ago by david.4.ray10 • updated 21 days ago by RamRS25k
0
votes
1
answer
3.5k
views
1
answers
Comment: C: BWA MEM indexing
... Yeah, I was afraid it might be something less simple.  It's interesting, though, because I previously successfully assembled the genome using bwa aln and exactly the same files that I'm using here.  The only difference is that I've switched to bwa mem.  Does that change your response at all? ...
written 4.2 years ago by david.4.ray10
0
votes
1
answer
3.5k
views
1
answer
BWA MEM indexing
... I'm a relative newbie and trying t work my way through using bwa mem.  I've successfully aligned PE reads to a reference genome previously using bwa aln but I thought this might work better. I'm getting the following output: [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, ...
assembly alignment written 4.2 years ago by david.4.ray10 • updated 4.2 years ago by Istvan Albert ♦♦ 81k

Latest awards to david.4.ray

Popular Question 3.7 years ago, created a question with more than 1,000 views. For BWA MEM indexing
Popular Question 3.7 years ago, created a question with more than 1,000 views. For [bcf_sync] incorrect number of fields (0 != 5) at 0:0

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1982 users visited in the last hour