SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 20 of 20
Search took 0.00 seconds.
Search: Posts Made By: mihuzx
Forum: Bioinformatics 11-18-2015, 11:57 PM
Replies: 0
Views: 1,031
Posted By mihuzx
how to filtering out SNPs on the same chromosome in complete linkage disequilibrium

Hi all,
I am a newbie in gwas study,
I want to filter out SNPs on the same chromosome in complete linkage disequilibrium, Is there a software can do this job?
Or any suggestion is very...
Forum: Bioinformatics 08-06-2014, 03:17 AM
Replies: 7
Views: 5,733
Posted By mihuzx
hi velt, thank you very much. I have...

hi velt,
thank you very much.
I have tried it with my data. the SERE score is 5.8.
and another pair replication is about 3.3
is this too high? or any sugguestions ?
by the...
Forum: RNA Sequencing 08-06-2014, 02:47 AM
Replies: 4
Views: 1,225
Posted By mihuzx
oh, I see, thank you very much!

oh, I see,
thank you very much!
Forum: RNA Sequencing 08-06-2014, 01:05 AM
Replies: 4
Views: 1,225
Posted By mihuzx
hi dpryan, thank you for your reply, I...

hi dpryan,
thank you for your reply,
I have read an artical for rnaseq written by ENCODE (the title is Standards, Guidelines and Best Practices for RNA-Seq),and they suguest that "A typical...
Forum: Bioinformatics 08-05-2014, 10:47 PM
Replies: 7
Views: 5,733
Posted By mihuzx
thank you for your advice, I removed all genes...

thank you for your advice,
I removed all genes < 10 and calculated the spearman correlation, but it still only about 0.93.
and I calculate spearson crrelation with genes < 1RPKM ,it didn't change....
Forum: RNA Sequencing 08-05-2014, 05:20 PM
Replies: 4
Views: 1,225
Posted By mihuzx
RNA-seq bio-replication with low correlation

Hi!
I sequeced two biological replicates for one condition with Hiseq 2000 platfom.
but the typical R(Pearson) correlation of gene expression(Raw Count) between two biological replicates is only...
Forum: Bioinformatics 08-05-2014, 04:52 PM
Replies: 7
Views: 5,733
Posted By mihuzx
Unhappy RNA-seq bio-replication with low correlation

Hi!
I sequeced two biological replicates for one condition with Hiseq 2000 platfom.
but the typical R(Pearson) correlation of gene expression(Raw Count) between two biological replicates is...
Forum: RNA Sequencing 05-10-2014, 07:10 AM
Replies: 3
Views: 1,946
Posted By mihuzx
maybe something wrong with the library...

maybe something wrong with the library construction.
can map the reads to ncbi db or rRNA db to check if the library is pure and no rRNA.
I am sorry my English is poor.Hope i made it clear.
Forum: RNA Sequencing 04-14-2014, 12:56 AM
Replies: 8
Views: 2,492
Posted By mihuzx
Smile thank you, It is really very useful for me!:D

thank you, It is really very useful for me!:D
Forum: RNA Sequencing 04-13-2014, 06:10 PM
Replies: 8
Views: 2,492
Posted By mihuzx
thank you for your reply, and I do need to learn...

thank you for your reply, and I do need to learn more about computer languages ,such as R,perl or something...
Forum: RNA Sequencing 04-12-2014, 05:10 PM
Replies: 8
Views: 2,492
Posted By mihuzx
Smile thank you very much. I am sorry for the wrong...

thank you very much. I am sorry for the wrong picture, but it just is a rarefaction plot.

is there any tool to draw a rarefaction plot? I am not good at computer language ,any software or script...
Forum: RNA Sequencing 04-12-2014, 05:44 AM
Replies: 8
Views: 2,492
Posted By mihuzx
Smile any tools to test if my RNAseq data is enough?

Hi,
I am new to the field of RNA sequencing.I have read a lot of message about how many reads is enough for RNAseq,but it seems that there is no exact answer.
Anyway, now I just wondering if...
Forum: Bioinformatics 02-18-2014, 03:36 AM
Replies: 3
Views: 1,507
Posted By mihuzx
thanks for your suggestion, I'll give it a try...

thanks for your suggestion, I'll give it a try later~
Forum: Bioinformatics 02-17-2014, 04:12 PM
Replies: 3
Views: 1,507
Posted By mihuzx
Blast+ Error: cannot get seq-data in range

Hi, everyone
I am using NCBI-BLAST-2.2.28+ to perform blastn-short blast for about 200 primers in one file. and The database is Zea mays genome(about 2Gb).
the standalone blast program work well in...
Forum: Bioinformatics 11-15-2013, 04:13 PM
Replies: 10
Views: 9,973
Posted By mihuzx
thanks for your quick and well-thought answer. ...

thanks for your quick and well-thought answer.
I was always thinking about how to get the low_mismatch.sam directly,but failed. now I know there so many things to lean for me.
thanks again for your...
Forum: Bioinformatics 11-15-2013, 02:29 AM
Replies: 10
Views: 9,973
Posted By mihuzx
thanks a lot. from the answer, I think out a...

thanks a lot. from the answer, I think out a another solution using perl. the code is :
perl -ne "print if /XM:i:[0-2]/;" raw.sam >cleaned.sam
Forum: Bioinformatics 11-12-2013, 03:58 PM
Replies: 10
Views: 9,973
Posted By mihuzx
Smile hi, had your problem been solved. but now i...

hi,
had your problem been solved. but now i meet the same problem, could you please tell me how you extract the reads no more than 2 mismatch?
thanks a lot.
Forum: Bioinformatics 11-11-2013, 02:13 AM
Replies: 0
Views: 1,731
Posted By mihuzx
Smile fastx-clipper to remove adapters problem

Hi everyone,
today I tried to remove adapters using fastx-cliper, it worked all right, but the result is a little confused. here is the situation:
first I check the sequence quality using fastqc,...
Forum: Bioinformatics 10-10-2013, 02:34 AM
Replies: 3
Views: 5,616
Posted By mihuzx
thanks for your advice. this is the exact...

thanks for your advice. this is the exact solution to my problem.
thanks to everyone.
Forum: Bioinformatics 10-09-2013, 05:55 PM
Replies: 3
Views: 5,616
Posted By mihuzx
Smile samtools mpipeup error: different line length in sequence 'chr1'.

hi,
I am new about samtools and bioinformatics, these days I try to call an SNP using bwa and samtools.everything went well, but at the last step, there is an error:
[fai_load] build FASTA...
Showing results 1 to 20 of 20

 


All times are GMT -8. The time now is 08:48 AM.


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