Originally posted by henry
View Post
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
about problems run into for samtools
Hi,guys,
I created tissue.sam file, using ./bwa samse. I tried to convert the tissue.sam file into tissue.bam, using ./samtools view -bt ref.fa.fai -o tissue.bam tissue.sam
But an error popped up. the error is as follows:
[sam_header_read2] 24 sequences loaded.
Parse error at line 1: invalid CIGAR character
Aborted
Could you kindly help me fix this problem? Thank you a lot.
Btw, I created the ref.fa.fai, using ./samtools faidx ref.fa
The content of the ref.fa.fai is as follows:
gi|224384768|gb|CM000663.1| 249250621 87 70 71
gi|224384767|gb|CM000664.1| 243199373 252811519 70 71
gi|224384766|gb|CM000665.1| 198022430 499485256 70 71
gi|224384765|gb|CM000666.1| 191154276 700336665 70 71
gi|224384764|gb|CM000667.1| 180915260 894221804 70 71
gi|224384763|gb|CM000668.1| 171115067 1077721655 70 71
gi|224384762|gb|CM000669.1| 159138663 1251281310 70 71
gi|224384761|gb|CM000670.1| 146364022 1412693470 70 71
gi|224384760|gb|CM000671.1| 141213431 1561148494 70 71
gi|224384759|gb|CM000672.1| 135534747 1704379348 70 71
gi|224384758|gb|CM000673.1| 135006516 1841850394 70 71
gi|224384757|gb|CM000674.1| 133851895 1978785663 70 71
gi|224384756|gb|CM000675.1| 115169878 2114549816 70 71
gi|224384755|gb|CM000676.1| 107349540 2231365066 70 71
gi|224384754|gb|CM000677.1| 102531392 2340248259 70 71
gi|224384753|gb|CM000678.1| 90354753 2444244474 70 71
gi|224384752|gb|CM000679.1| 81195210 2535890098 70 71
gi|224384751|gb|CM000680.1| 78077248 2618245328 70 71
gi|224384750|gb|CM000681.1| 59128983 2697438054 70 71
gi|224384749|gb|CM000682.1| 63025520 2757411825 70 71
gi|224384748|gb|CM000683.1| 48129895 2821337798 70 71
gi|224384747|gb|CM000684.1| 51304566 2870155351 70 71
gi|224384746|gb|CM000685.1| 155270560 2922192927 70 71
gi|224384745|gb|CM000686.1| 59373566 3079681725 70 71Tags: None
Latest Articles
Collapse
-
by seqadmin
The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...-
Channel: Articles
Today, 07:48 AM -
-
by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
Channel: Articles
04-22-2024, 07:01 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Today, 07:17 AM
|
0 responses
11 views
0 likes
|
Last Post
by seqadmin
Today, 07:17 AM
|
||
Started by seqadmin, 05-02-2024, 08:06 AM
|
0 responses
19 views
0 likes
|
Last Post
by seqadmin
05-02-2024, 08:06 AM
|
||
Started by seqadmin, 04-30-2024, 12:17 PM
|
0 responses
20 views
0 likes
|
Last Post
by seqadmin
04-30-2024, 12:17 PM
|
||
Started by seqadmin, 04-29-2024, 10:49 AM
|
0 responses
28 views
0 likes
|
Last Post
by seqadmin
04-29-2024, 10:49 AM
|
Leave a comment: